Pypath inputs status report

Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.

Compiled between 2022-05-05 00:48:01 and 2022-05-05 07:03:56; pypath version: 0.14.9 (from git; feb28f6 )

Modules collected: 152
Modules failed to import: 2
Functions collected: 477
Functions run without error: 328
Functions returned empty value: 10
Functions skipped due to lack of arguments: 120
Functions run with error: 29

Function Started Finished Elapsed (s) Result type Result repr Result size Error Change since last time Last succeeded
pypath.inputs.abs.abs_interactions 2022-05-05 00:48:09 2022-05-05 00:48:10 0.46 list [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) 650 {} 2022-05-05 00:48:09
pypath.inputs.acsn.acsn_interactions 2022-05-05 00:48:10 2022-05-05 00:48:12 2.00 list [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) 37,725 {} 2022-05-05 00:48:10
pypath.inputs.acsn.acsn_interactions_sif 2022-05-05 00:48:12 2022-05-05 00:48:12 0.43 list [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) 9,570 {} 2022-05-05 00:48:12
pypath.inputs.adhesome.adhesome_annotations 2022-05-05 00:48:12 2022-05-05 00:50:17 124.43 dict {'P12814': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'P23528': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q9BR76': {AdhesomeAnnotation(mainclass='Actin regulation', intrinsic=True)}, 'Q14247': {AdhesomeAnnotation(mainclass='Actin regulation', intri...(truncated) 239 {} 2022-05-05 00:48:12
pypath.inputs.adhesome.adhesome_interactions 2022-05-05 00:50:17 2022-05-05 00:50:25 8.18 list [AdhesomeInteraction(source='LPXN', target='GIT1', effect='0', type='Binding', pmid='12674328'), AdhesomeInteraction(source='GIT1', target='ARF1', effect='_', type='Inhibition', pmid='10896954'), AdhesomeInteraction(source='ARPC2', target='CTTN', effect='0', type='Binding', pmid='11018051'), Adhesom...(truncated) 6,542 {'size': -1184} 2022-05-05 00:50:17
pypath.inputs.almen2009.almen2009_annotations 2022-05-05 00:50:25 2022-05-05 00:50:29 4.09 dict {'P04839': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembrane=5, tmhmm_transmembrane=4)}, 'Q9Y5S8': {Almen2009Annotation(mainclass='Enzymes', classes=('1',), phobius_secreted=False, phobius_transmembrane=5, sosui_transmembra...(truncated) 4,826 {} 2022-05-05 00:50:25
pypath.inputs.baccin2019.baccin2019_annotations 2022-05-05 00:50:29 2022-05-05 00:53:36 186.86 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 196, in baccin2019_annotations
    ia_all = baccin2019_interactions(ncbi_tax_id = ncbi_tax_id)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
    ligand_components = raw_to_uniprots(rec[1])
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
    itertools.product(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 85, in <genexpr>
    *(id_translate(comp) for comp in components)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 66, in id_translate
    itertools.chain(*(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 67, in <genexpr>
    homology_mod.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 1187, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 258, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 172, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 203, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 213, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 485, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 501, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 640, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 94, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-04-29 00:52:59
pypath.inputs.baccin2019.baccin2019_interactions 2022-05-05 00:53:36 2022-05-05 00:55:11 94.89 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 137, in baccin2019_interactions
    ligand_components = raw_to_uniprots(rec[1])
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 84, in raw_to_uniprots
    itertools.product(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 85, in <genexpr>
    *(id_translate(comp) for comp in components)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 66, in id_translate
    itertools.chain(*(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/baccin2019.py", line 67, in <genexpr>
    homology_mod.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 1187, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 258, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 172, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 203, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 213, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 485, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 501, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 640, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 94, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-04-30 00:59:46
pypath.inputs.biogps.biogps_datasets 2022-05-05 00:55:11 2022-05-05 00:55:11 0.00 list [BiogpsDataset(organism='human', label='human_gene_atlas_ave', url='http://plugins.biogps.org/download/gnf1h-gcrma.zip'), BiogpsDataset(organism='human', label='human_gene_atlas', url='http://plugins.biogps.org/download/gnf1h-gcrma-unaveraged.zip'), BiogpsDataset(organism='human', label='human_nci60...(truncated) 9 {} 2022-05-05 00:55:11
pypath.inputs.biogps.biogps_download 
Not calling `pypath.inputs.biogps.biogps_download`, not enough arguments.
 {} never
pypath.inputs.biogps.biogps_download_all 2022-05-05 00:55:11 2022-05-05 01:01:20 369.82 dict {'human_gene_atlas_ave': probe B_lymphoblasts ... retina small_intestine 0 1007_s_at 137.00 ... 880.675 168.15 1 1053_at 81.75 ... 9.900 8.50 2 117_at 12.55 ...(truncated) 9 {} 2022-05-05 00:55:11
pypath.inputs.biogrid.biogrid_all_interactions 2022-05-05 01:01:21 2022-05-05 01:08:36 434.45 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/biogrid.py", line 141, in biogrid_all_interactions
    f = next(iter(c.result.values()))
AttributeError: 'NoneType' object has no attribute 'values'
{} 2022-04-01 00:28:58
pypath.inputs.biogrid.biogrid_interactions 2022-05-05 01:08:36 2022-05-05 01:08:37 0.99 list [BiogridPhysicalInteraction(partner_a='APOB', partner_b='MTTP', pmid='9915855'), BiogridPhysicalInteraction(partner_a='CAPN3', partner_b='TTN', pmid='9642272'), BiogridPhysicalInteraction(partner_a='DOCK8', partner_b='CDC42', pmid='15304341'), BiogridPhysicalInteraction(partner_a='CDKN3', partner_b=...(truncated) 6,698 {} 2022-05-05 01:08:36
pypath.inputs.biomart.biomart_homology 2022-05-05 01:08:37 2022-05-05 01:09:07 30.54 list [EnsemblRecord(ensembl_gene_id='ENSG00000198888', ensembl_transcript_id='ENST00000361390', ensembl_peptide_id='ENSP00000354687', mmusculus_homolog_ensembl_peptide='ENSMUSP00000080991', mmusculus_homolog_ensembl_gene='ENSMUSG00000064341', mmusculus_homolog_orthology_type='ortholog_one2one', mmusculus...(truncated) 176,673 {} 2022-05-05 01:08:37
pypath.inputs.biomart.biomart_microarray 
Not calling `pypath.inputs.biomart.biomart_microarray`, not enough arguments.
 {} never
pypath.inputs.biomart.biomart_microarray_types 2022-05-05 01:09:07 2022-05-05 01:09:08 0.30 list [{'description': None, 'type': 'OLIGO', 'vendor': 'PHALANX', 'format': 'EXPRESSION', 'array': 'OneArray', 'label': 'PHALANX OneArray'}, {'description': None, 'type': 'OLIGO', 'vendor': 'CODELINK', 'format': 'EXPRESSION', 'array': 'CODELINK', 'label': 'CODELINK CODELINK'}, {'format': 'EXPRESSION', 'a...(truncated) 39 {} 2022-05-05 01:09:07
pypath.inputs.biomart.biomart_query 
Not calling `pypath.inputs.biomart.biomart_query`, not enough arguments.
 {} never
pypath.inputs.ca1.ca1_interactions 2022-05-05 01:09:08 2022-05-05 01:09:10 2.69 list [Ca1Interaction(genesymbol_source='GLYCINE', uniprot_source='NA', uniprot_mouse_source='NA', function_source='Ligand', location_source='Extracellular', genesymbol_target='NMDAR', uniprot_target='Q12879', uniprot_mouse_target='P35436', function_target='Receptor', location_target='Membrane', effect='+...(truncated) 1,788 {} 2022-05-05 01:09:08
pypath.inputs.cancercellmap.ccmap_interactions 2022-05-05 01:09:10 2022-05-05 01:09:11 0.91 list [CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q96S28', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q86YA7', directed=False, references='15262978'), CancercellmapInteraction(source_uniprot='Q5VTT9', target_uniprot='Q4T...(truncated) 47,644 {} 2022-05-05 01:09:10
pypath.inputs.cancerdrugs_db.cancerdrugs_db_annotations 2022-05-05 01:09:11 2022-05-05 01:09:24 13.05 defaultdict defaultdict(<class 'set'>, {'46220502': {CancerDrugsAnnotation(label='Abemaciclib', indications='Advanced Breast Cancer; Metastatic Breast Cancer', last_updated='01/02/2022')}, '132971': {CancerDrugsAnnotation(label='Abiraterone', indications='Metastatic Castration Resistant Prostate Cancer', last_u...(truncated) 200 {} 2022-05-05 01:09:11
pypath.inputs.cancerdrugs_db.cancerdrugs_db_download 2022-05-05 01:09:24 2022-05-05 01:09:24 0.00 list [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) 284 {} 2022-05-05 01:09:24
pypath.inputs.cancerdrugs_db.cancerdrugs_db_interactions 2022-05-05 01:09:24 2022-05-05 01:09:25 1.02 list [CancerDrugsInteraction(source={'46220502'}, target={'Q00534'}), CancerDrugsInteraction(source={'46220502'}, target={'P11802'}), CancerDrugsInteraction(source={'46220502'}, target={'P24385'}), CancerDrugsInteraction(source={'46220502'}, target={'P30281'}), CancerDrugsInteraction(source={'46220502'},...(truncated) 2,864 {} 2022-05-05 01:09:24
pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations 2022-05-05 01:09:25 2022-05-05 01:09:26 0.15 dict {'46220502': {CancerdrugsdbAnnotation(drug_label='Abemaciclib', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Advanced Breast Cancer', 'Metastatic Breast Cancer'))}, '132971': {CancerdrugsdbAnnotation(drug...(truncated) 188 {} 2022-05-05 01:09:25
pypath.inputs.cancerdrugsdb.cancerdrugsdb_download 2022-05-05 01:09:26 2022-05-05 01:09:26 0.00 list [{'Product': 'Abemaciclib', 'EMA': 'Y', 'FDA': 'Y', 'EN': 'N', 'Other': '', 'WHO': 'N', 'Year': '2017', 'Generic': 'N', 'DrugBank ID': '<a href="https://go.drugbank.com/drugs/DB12001">DB12001</a>', 'ATC': 'L01EF03', 'ChEMBL': '<a href="https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL3301610"...(truncated) 284 {} 2022-05-05 01:09:26
pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions 2022-05-05 01:09:26 2022-05-05 01:09:26 0.14 list [CancerdrugsdbInteraction(drug_pubchem='46220502', drug_chembl='CHEMBL3301610', drug_drugbank='DB12001', drug_label='Abemaciclib', target_uniprot='Q8N726', ema_approved=True, fda_approved=True, european_national_approved=False, who_approved=False, generic=False, approval_year=2017, indications=('Adv...(truncated) 2,378 {} 2022-05-05 01:09:26
pypath.inputs.cancersea.cancersea_annotations 2022-05-05 01:09:26 2022-05-05 01:09:27 1.72 dict {'P37023': {CancerseaAnnotation(state='Angiogenesis')}, 'P78504': {CancerseaAnnotation(state='Angiogenesis'), CancerseaAnnotation(state='Metastasis'), CancerseaAnnotation(state='Inflammation')}, 'Q15389': {CancerseaAnnotation(state='Angiogenesis')}, 'O15123': {CancerseaAnnotation(state='Angiogenesis...(truncated) 1,247 {} 2022-05-05 01:09:26
pypath.inputs.cell.cell_supplementary 
Not calling `pypath.inputs.cell.cell_supplementary`, not enough arguments.
 {} never
pypath.inputs.cellcall.cellcall_annotations 2022-05-05 01:09:27 2022-05-05 01:09:35 7.61 dict {'P08476': {CellcallAnnotation(role='ligand')}, 'Q8NER5': {CellcallAnnotation(role='receptor')}, 'P78504': {CellcallAnnotation(role='ligand')}, 'P46531': {CellcallAnnotation(role='receptor')}, 'Q9GZV9': {CellcallAnnotation(role='ligand')}, 'P21802': {CellcallAnnotation(role='receptor')}, 'O00175': {...(truncated) 460 {} 2022-05-05 01:09:27
pypath.inputs.cellcall.cellcall_download 2022-05-05 01:09:35 2022-05-05 01:09:35 0.04 list [{'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '2626', 'Pathway': 'hsa04530_3,hsa04530_5', 'pathway_ID': 'hsa04530', 'Ligand_Symbol': 'OCLN', 'Receptor_Symbol': 'OCLN', 'TF_Symbol': 'GATA4'}, {'Ligand_ID': '100506658', 'Receptor_ID': '100506658', 'TF_ID': '8531', 'Pathway': 'hsa045...(truncated) 19,144 {} 2022-05-05 01:09:35
pypath.inputs.cellcall.cellcall_download_all 2022-05-05 01:09:35 2022-05-05 01:09:36 0.94 list [{'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '16150', 'Pathway': 'hsa04062_5', 'pathway_ID': 'hsa04062', 'Ligand_Symbol': 'Cxcl13', 'Receptor_Symbol': 'Xcr1', 'TF_Symbol': 'Ikbkb', 'extended': True, 'organism': 10090}, {'Ligand_ID': '55985', 'Receptor_ID': '23832', 'TF_ID': '18033', 'Pat...(truncated) 38,645 {} 2022-05-05 01:09:35
pypath.inputs.cellcall.cellcall_interactions 2022-05-05 01:09:36 2022-05-05 01:09:38 1.74 list [CellcallInteraction(ligand_uniprot='P08476', receptor_uniprot='Q8NER5', core=True), CellcallInteraction(ligand_uniprot='P78504', receptor_uniprot='P46531', core=True), CellcallInteraction(ligand_uniprot='Q9GZV9', receptor_uniprot='P21802', core=True), CellcallInteraction(ligand_uniprot='O00175', re...(truncated) 797 {} 2022-05-05 01:09:36
pypath.inputs.cellcellinteractions.cellcellinteractions_annotations 2022-05-05 01:09:38 2022-05-05 01:09:39 0.93 dict {'Q8IVN8': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), CellcellinteractionsAnnotation(mainclass='ECM')}, 'O95967': {CellcellinteractionsAnnotation(mainclass='Receptor'), CellcellinteractionsAnnotation(mainclass='Ligand'), Cellcellinterac...(truncated) 3,425 {} 2022-05-05 01:09:38
pypath.inputs.cellchatdb._cellchatdb_organism 2022-05-05 01:09:39 2022-05-05 01:09:39 0.00 int 9606 0 {} 2022-05-05 01:09:39
pypath.inputs.cellchatdb._cellchatdb_process_cofactors 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_cofactors`, not enough arguments.
 {} never
pypath.inputs.cellchatdb._cellchatdb_process_complexes 
Not calling `pypath.inputs.cellchatdb._cellchatdb_process_complexes`, not enough arguments.
 {} never
pypath.inputs.cellchatdb.cellchatdb_annotations 2022-05-05 01:09:39 2022-05-05 01:09:46 7.40 dict {'P01137': {CellChatDBAnnotation(role='ligand', pathway='TGFb', category='Secreted Signaling')}, Complex TGFbR1_R2: COMPLEX:P36897_P37173: {CellChatDBAnnotation(role='receptor', pathway='TGFb', category='Secreted Signaling')}, 'P19883': {CellChatDBAnnotation(role='antagonist', pathway='ACTIVIN', cat...(truncated) 1,067 {} 2022-05-05 01:09:39
pypath.inputs.cellchatdb.cellchatdb_cofactors 2022-05-05 01:09:46 2022-05-05 01:09:51 4.97 dict {'ACTIVIN antagonist': {'P19883'}, 'ACTIVIN inhibition receptor': {'Q13145'}, 'ANGPT inhibition receptor 1': {'P35590'}, 'ANGPT inhibition receptor 2': {'P23467'}, 'BMP antagonist': {'O60565', 'P41271', 'Q9H772', 'Q13253', 'P12645', 'O00292', 'O75610', 'Q9H2X0'}, 'BMP inhibition receptor': {'Q13145'...(truncated) 31 {} 2022-05-05 01:09:46
pypath.inputs.cellchatdb.cellchatdb_complexes 2022-05-05 01:09:51 2022-05-05 01:09:56 5.09 dict {'COMPLEX:P08476_P09529': Complex Activin AB: COMPLEX:P08476_P09529, 'COMPLEX:P05111_P08476': Complex Inhibin A: COMPLEX:P05111_P08476, 'COMPLEX:P05111_P09529': Complex Inhibin B: COMPLEX:P05111_P09529, 'COMPLEX:P29459_P29460': Complex IL12AB: COMPLEX:P29459_P29460, 'COMPLEX:P29460_Q9NPF7': Complex ...(truncated) 153 {} 2022-05-05 01:09:51
pypath.inputs.cellchatdb.cellchatdb_download 2022-05-05 01:09:56 2022-05-05 01:10:01 4.47 dict {'interaction': interaction_name ... rownames TGFB1_TGFBR1_TGFBR2 TGFB1_TGFBR1_TGFBR2 ... TGFB1_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 TGFB2_TGFBR1_TGFBR2 ... TGFB2_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 TGFB3_TGFBR1_TGFBR2 ... TGFB3_TGFBR1_TGFBR2 TGFB1_ACVR1B_TGF...(truncated) 4 {} 2022-05-05 01:09:56
pypath.inputs.cellchatdb.cellchatdb_interactions 2022-05-05 01:10:01 2022-05-05 01:10:06 4.80 list [CellChatDBInteraction(id_a='P01137', id_b=Complex TGFbR1_R2: COMPLEX:P36897_P37173, role_a='ligand', role_b='receptor', effect='unknown', pathway='TGFb', refs=[], category='Secreted Signaling'), CellChatDBInteraction(id_a='P19883', id_b='P01137', role_a='agonist', role_b='ligand', effect='stimulati...(truncated) 11,113 {} 2022-05-05 01:10:01
pypath.inputs.cellinker._cellinker_interactions_raw 2022-05-05 01:10:06 2022-05-05 01:10:06 0.28 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2022-05-05 01:10:06
pypath.inputs.cellinker._cellinker_uniprots 
Not calling `pypath.inputs.cellinker._cellinker_uniprots`, not enough arguments.
 {} never
pypath.inputs.cellinker.cellinker_annotations 2022-05-05 01:10:06 2022-05-05 01:10:07 0.83 dict {'P14138': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'P24530': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='...(truncated) 1,921 {} 2022-05-05 01:10:06
pypath.inputs.cellinker.cellinker_complex_annotations 2022-05-05 01:10:07 2022-05-05 01:10:08 0.74 dict {Complex: COMPLEX:P06756_P26012: {CellinkerAnnotation(role='receptor', location='Membrane', type='ECM-receptor interaction')}, Complex: COMPLEX:P27037_Q8NER5: {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction')}, Complex: COMPLEX:O75084_O75581:...(truncated) 134 {} 2022-05-05 01:10:07
pypath.inputs.cellinker.cellinker_complexes 2022-05-05 01:10:08 2022-05-05 01:10:08 0.03 dict {'COMPLEX:O75462_Q9UBD9': Complex: COMPLEX:O75462_Q9UBD9, 'COMPLEX:P14770_P40197': Complex: COMPLEX:P14770_P40197, 'COMPLEX:P01857_P0CG04': Complex: COMPLEX:P01857_P0CG04, 'COMPLEX:P29460_Q9NPF7': Complex: COMPLEX:P29460_Q9NPF7, 'COMPLEX:P29459_Q8NEV9': Complex: COMPLEX:P29459_Q8NEV9, 'COMPLEX:Q0477...(truncated) 143 {} 2022-05-05 01:10:08
pypath.inputs.cellinker.cellinker_complexes_raw 2022-05-05 01:10:08 2022-05-05 01:10:08 0.00 list [CellinkerComplex(role='ligand', cellinker_id='CH0131', components=(CellinkerComplexComponent(genesymbol='CRLF1', entrez='9244'), CellinkerComplexComponent(genesymbol='CLCF1', entrez='23529')), location='Secreted'), CellinkerComplex(role='ligand', cellinker_id='CH0132', components=(CellinkerComplexC...(truncated) 145 {} 2022-05-05 01:10:08
pypath.inputs.cellinker.cellinker_lr_interactions 2022-05-05 01:10:08 2022-05-05 01:10:08 0.74 set {CellinkerInteraction(ligand='P14138', receptor='P24530', ligand_location='Secreted', receptor_location='Membrane', resources='HPMR;Guide2Pharma', pmids='8904635;8460684;11982704;8086489;8001160;7524189', type='Secreted protein to receptor interaction'), CellinkerInteraction(ligand='Q8TEW0', recepto...(truncated) 3,812 {} 2022-05-05 01:10:08
pypath.inputs.cellinker.cellinker_lr_interactions_raw 2022-05-05 01:10:08 2022-05-05 01:10:08 0.01 list [{'Ligand_id': '1000', 'Ligand_symbol': 'CDH2', 'Ligand_location': 'Membrane', 'Receptor_id': '1000', 'Receptor_symbol': 'CDH2', 'Receptor.location': 'Membrane', 'Type': 'Cell adhesion', 'KEGG.pathway': 'hsa04514:Cell adhesion molecules (CAMs)', 'Pmubmed.ID': '32196115', 'Other.DB': '', 'LRID': 'LR0...(truncated) 3,744 {} 2022-05-05 01:10:08
pypath.inputs.cellinker.cellinker_protein_annotations 2022-05-05 01:10:08 2022-05-05 01:10:09 0.74 dict {'P14138': {CellinkerAnnotation(role='ligand', location='Secreted', type='Secreted protein to receptor interaction')}, 'P24530': {CellinkerAnnotation(role='receptor', location='Membrane', type='Secreted protein to receptor interaction'), CellinkerAnnotation(role='ligand', location='Membrane', type='...(truncated) 1,787 {} 2022-05-05 01:10:08
pypath.inputs.cellinker.cellinker_smol_interactions 2022-05-05 01:10:09 2022-05-05 01:10:09 0.22 set {CellinkerInteraction(ligand='6435286', receptor='Q13304', ligand_location=None, receptor_location='Membrane', resources='Guide2Pharma', pmids='16990797', type='sMOL-receptor interaction'), CellinkerInteraction(ligand='187', receptor='P20309', ligand_location=None, receptor_location='Membrane', reso...(truncated) 314 {} 2022-05-05 01:10:09
pypath.inputs.cellinker.cellinker_smol_interactions_raw 2022-05-05 01:10:09 2022-05-05 01:10:09 0.00 list [{'ligand_pubchem_sid': '135651413', 'ligand_pubchem_cid': '5202', 'ligand name': '5-hydroxytryptamine', 'ligand_type': 'Metabolite', 'Receptor_id': '3350', 'Receptor_symbol': 'HTR1A', 'Receptor_uniprot': 'P08908', 'Receptor_location': 'Membrane', 'Type': 'sMOL-receptor interaction', 'target_species...(truncated) 341 {} 2022-05-05 01:10:09
pypath.inputs.cellinker.components_to_complex 
Not calling `pypath.inputs.cellinker.components_to_complex`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_annotations 
Not calling `pypath.inputs.cellphonedb._cellphonedb_annotations`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_get_entity 
Not calling `pypath.inputs.cellphonedb._cellphonedb_get_entity`, not enough arguments.
 {} never
pypath.inputs.cellphonedb._cellphonedb_hla 
Not calling `pypath.inputs.cellphonedb._cellphonedb_hla`, not enough arguments.
 {} never
pypath.inputs.cellphonedb.cellphonedb_complex_annotations 2022-05-05 01:10:09 2022-05-05 01:10:10 0.23 dict {Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('receptor',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873: CellPhoneDBAnnotation(receptor=True, receptor_class=('...(truncated) 112 {} 2022-05-05 01:10:09
pypath.inputs.cellphonedb.cellphonedb_complexes 2022-05-05 01:10:10 2022-05-05 01:10:10 0.02 dict {'COMPLEX:P37023_Q13873': Complex ACVL1_BMPR2: COMPLEX:P37023_Q13873, 'COMPLEX:Q04771_Q13873': Complex ACVR1_BMPR2: COMPLEX:Q04771_Q13873, 'COMPLEX:P27037_Q04771': Complex ACVR_1A2A receptor: COMPLEX:P27037_Q04771, 'COMPLEX:Q04771_Q13705': Complex ACVR_1A2B receptor: COMPLEX:Q04771_Q13705, 'COMPLEX:...(truncated) 112 {} 2022-05-05 01:10:10
pypath.inputs.cellphonedb.cellphonedb_interactions 2022-05-05 01:10:10 2022-05-05 01:10:10 0.60 list [CellphonedbInteraction(id_a=Complex IL12: COMPLEX:P29459_P29460, id_b=Complex IL12 receptor: COMPLEX:P42701_Q99665, sources='CellPhoneDB', references='', interaction_type='ligand-receptor', type_a='ligand', type_b='receptor'), CellphonedbInteraction(id_a=Complex Activin ligand ab: COMPLEX:P08476_P0...(truncated) 1,396 {} 2022-05-05 01:10:10
pypath.inputs.cellphonedb.cellphonedb_ligands_receptors 2022-05-05 01:10:10 2022-05-05 01:10:10 0.06 tuple ({'P09341', 'P01222', 'O00755', Complex aVb3 complex: COMPLEX:P05106_P06756, 'Q9P0W0', 'P0DMC3', 'P08174', 'P98172', 'Q08345', 'P10600', 'Q93038', 'Q14406', 'O60383', 'P12830', 'P41273', 'Q07325', 'O00548', 'P52803', 'P01584', 'O00253', 'P01563', 'P30511', 'O60258', 'P02778', 'Q9BYF1', 'P49961', 'P5...(truncated) 2 {} 2022-05-05 01:10:10
pypath.inputs.cellphonedb.cellphonedb_protein_annotations 2022-05-05 01:10:10 2022-05-05 01:10:10 0.06 dict {'A4D1S0': CellPhoneDBAnnotation(receptor=True, receptor_class=('klr',), peripheral=False, secreted=False, secreted_class=(), transmembrane=True, integrin=False), 'A6NMZ7': CellPhoneDBAnnotation(receptor=False, receptor_class=(), peripheral=False, secreted=True, secreted_class=('secreted',), transme...(truncated) 978 {} 2022-05-05 01:10:10
pypath.inputs.celltalkdb.celltalkdb_annotations 2022-05-05 01:10:10 2022-05-05 01:10:23 12.27 dict {'Q13275': {CellTalkDBAnnotation(role='ligand', pmid='26156437'), CellTalkDBAnnotation(role='ligand', pmid='9883722'), CellTalkDBAnnotation(role='ligand', pmid='15721238')}, 'P51805': {CellTalkDBAnnotation(role='receptor', pmid='32196115'), CellTalkDBAnnotation(role='receptor', pmid='15721238')}, 'Q...(truncated) 1,598 {} 2022-05-05 01:10:10
pypath.inputs.celltalkdb.celltalkdb_download 2022-05-05 01:10:23 2022-05-05 01:10:23 0.00 list [CellTalkDbRecord(lr_pair='SEMA3F_PLXNA3', ligand_gene_symbol='SEMA3F', receptor_gene_symbol='PLXNA3', ligand_gene_id='6405', receptor_gene_id='55558', ligand_ensembl_protein_id='ENSP00000002829', receptor_ensembl_protein_id='ENSP00000358696', ligand_ensembl_gene_id='ENSG00000001617', receptor_ensem...(truncated) 3,398 {} 2022-05-05 01:10:23
pypath.inputs.celltalkdb.celltalkdb_interactions 2022-05-05 01:10:23 2022-05-05 01:10:23 0.01 list [CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA3', reference='15721238'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='PLXNA1', reference='26156437'), CellTalkDBInteraction(ligand_genesymbol='SEMA3F', receptor_genesymbol='NRP1', reference='9883...(truncated) 3,398 {} 2022-05-05 01:10:23
pypath.inputs.celltypist.celltypist_annotations 2022-05-05 01:10:23 2022-05-05 01:10:23 0.29 dict {'P11836': {CelltypistAnnotation(cell_type='B cells', cell_subtype='Memory B cells', cell_ontology='CL:0000787', marker_type='curated_marker', tissues=('Blood', 'Bone marrow', 'Colon', 'Decidua', 'Lung', 'Lung-draining lymph node', 'Mesenteric lymph node', 'Oesophagus', 'Omentum adipose tissue', 'Sp...(truncated) 424 {} 2022-05-05 01:10:23
pypath.inputs.compleat.compleat_complexes 2022-05-05 01:10:23 2022-05-05 01:10:28 5.09 dict {'COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0': Complex: COMPLEX:O00161_O14662_O15400_O43752_O75379_P0CG48_P46459_P51809_P54920_Q12846_Q15836_Q8N1B4_Q96AJ9_Q9BV40_Q9UNK0, 'COMPLEX:O43681_O75396_P0CG48_P11441_Q7L5D6_Q8NEP3_Q96DZ5_Q9...(truncated) 9,693 {} 2022-05-05 01:10:23
pypath.inputs.compleat.compleat_raw 2022-05-05 01:10:28 2022-05-05 01:10:28 0.04 list [{'compleat_id': 'HC4831', 'member_count': '15', 'predicted': 'Predicted', 'functions': 'protein transport', 'functions2': 'protein transport;cellular membrane fusion;Golgi vesicle transport;vesicle-mediated transport;intracellular transport', 'nothing': '', 'sources': 'NetworkBlast', 'name': '', 'm...(truncated) 9,704 {} 2022-05-05 01:10:28
pypath.inputs.complexportal.complexportal_complexes 2022-05-05 01:10:28 2022-05-05 01:11:17 48.49 dict {'COMPLEX:P84022_Q13485_Q15796': Complex SMAD2-SMAD3-SMAD4 complex: COMPLEX:P84022_Q13485_Q15796, 'COMPLEX:P16220_P18848': Complex bZIP transcription factor complex, ATF4-CREB1: COMPLEX:P16220_P18848, 'COMPLEX:P18846_P18848': Complex bZIP transcription factor complex, ATF1-ATF4: COMPLEX:P18846_P1884...(truncated) 1,261 {} 2022-05-05 01:10:28
pypath.inputs.comppi.comppi_interaction_locations 2022-05-05 01:11:17 2022-05-05 01:12:23 66.80 list [ComppiInteraction(id_a='Q8TES7', id_b='O75478', loc_a=(ComppiLocation(location='cytosol', score=0.8), ComppiLocation(location='nucleus', score=0.7)), loc_b=(ComppiLocation(location='nucleus', score=0.8),)), ComppiInteraction(id_a='Q8TES7', id_b='O75478', loc_a=(ComppiLocation(location='cytosol', sc...(truncated) 591,078 {} 2022-05-05 01:11:17
pypath.inputs.comppi.comppi_locations 2022-05-05 01:12:23 2022-05-05 01:13:33 69.81 dict {'Q8TES7': {ComppiLocation(location='cytosol', score=0.9099999999999999), ComppiLocation(location='nucleus', score=0.9099999999999999), ComppiLocation(location='cytosol', score=0.99997984), ComppiLocation(location='membrane', score=0.96), ComppiLocation(location='nucleus', score=0.7), ComppiLocation...(truncated) 18,209 {} 2022-05-05 01:12:23
pypath.inputs.connectomedb.connectomedb_annotations 2022-05-05 01:13:33 2022-05-05 01:13:34 0.59 dict {'P01023': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'Q07954': {ConnectomedbAnnotation(role='receptor', location='plasma membrane')}, 'Q16613': {ConnectomedbAnnotation(role='ligand', location='secreted')}, 'P48039': {ConnectomedbAnnotation(role='receptor', location='plasma membra...(truncated) 1,428 {} 2022-05-05 01:13:33
pypath.inputs.connectomedb.connectomedb_interactions 2022-05-05 01:13:34 2022-05-05 01:13:34 0.01 list [ConnectomedbInteraction(ligand='A2M', ligand_location=['secreted'], receptor='LRP1', references=['1702392', '10652313', '12194978']), ConnectomedbInteraction(ligand='AANAT', ligand_location=['secreted'], receptor='MTNR1A', references=['12943195']), ConnectomedbInteraction(ligand='AANAT', ligand_loc...(truncated) 2,293 {} 2022-05-05 01:13:34
pypath.inputs.corum.corum_complexes 2022-05-05 01:13:34 2022-05-05 01:13:35 0.77 dict {'COMPLEX:P41182_P56524': Complex BCL6-HDAC4 complex: COMPLEX:P41182_P56524, 'COMPLEX:P41182_Q9UQL6': Complex BCL6-HDAC5 complex: COMPLEX:P41182_Q9UQL6, 'COMPLEX:P41182_Q8WUI4': Complex BCL6-HDAC7 complex: COMPLEX:P41182_Q8WUI4, 'COMPLEX:Q09472_Q92793_Q92831_Q9Y6Q9': Complex Multisubunit ACTR coacti...(truncated) 2,734 {} 2022-05-05 01:13:34
pypath.inputs.cosmic.cancer_gene_census_annotations 2022-05-05 01:13:35 2022-05-05 01:13:38 3.29 dict {'Q9NQ94': {CancerGeneCensusAnnotation(tier=2, hallmark=False, somatic=True, germline=False, tumour_types_somatic=('melanoma',), tumour_types_germline=(), cancer_syndrome=(), tissue_type=('E',), genetics=None, role=('oncogene',), mutation_type=('Mis',))}, 'Q8IZP0': {CancerGeneCensusAnnotation(tier=1...(truncated) 726 {} 2022-05-05 01:13:35
pypath.inputs.cpad.cpad_annotations 2022-05-05 01:13:38 2022-05-05 01:13:44 6.03 dict {'Q16181': {CpadAnnotation(regulator_type='protein', effect_on_pathway='Upregulation', pathway='Actin cytoskeleton pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration', cancer='Glioma', pathway_category='Regulation of actin cytoskeleton')}, 'MIMAT0000431'...(truncated) 1,037 {'size': -1} 2022-05-05 01:13:38
pypath.inputs.cpad.cpad_pathway_cancer 2022-05-05 01:13:44 2022-05-05 01:13:44 0.05 tuple ({'Glioma': {CpadPathwayCancer(pathway='NF-kappa B signaling pathway', cancer='Glioma', pathway_category='NF-kappa B signaling pathway', effect_on_cancer='Inhibiting', effect_on_cancer_outcome='inhibit glioma cell migration, invasion, and EMT'), CpadPathwayCancer(pathway='ROCK-FAK pathway', cancer='...(truncated) 2 {} 2022-05-05 01:13:44
pypath.inputs.cpad.get_cpad 2022-05-05 01:13:44 2022-05-05 01:13:44 0.04 list [{'Regulator': 'NULL', 'Regulator_Type': 'NULL', 'Pathway': '5-LO/LTA4 hydrolase pathway', 'Pathway_Category': 'Others', 'KEGG_ID': 'NULL', 'Regulation_Type': 'Inhibiting', 'Cancer': 'Glioma', 'ID': 'H00042', 'Outcome_Description': 'partial suppression of tumor growth', 'Description': 'We confirmed ...(truncated) 4,709 {} 2022-05-05 01:13:44
pypath.inputs.cpdb.cpdb_interactions 2022-05-05 01:13:44 2022-05-05 01:14:14 30.16 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 531,371 {} 2022-05-05 01:13:44
pypath.inputs.cpdb.cpdb_interactions_ltp 2022-05-05 01:14:14 2022-05-05 01:14:17 2.26 list [['SUMF2_HUMAN', 'SUMF1_HUMAN', 'Reactome', ''], ['ANPRA_HUMAN', 'ANF_HUMAN', 'PhosphoPOINT,Reactome,HPRD,Spike,Biogrid', '1660465,16713569,12547834'], ['ANFC_HUMAN', 'ANPRB_HUMAN', 'HPRD,Reactome,PhosphoPOINT,Biogrid', '1660465,12709393,1672777,1309330'], ['STIM1_HUMAN', 'TRPC1_HUMAN', 'DIP,Reactom...(truncated) 482,222 {} 2022-05-05 01:14:14
pypath.inputs.cspa.cspa_annotations 2022-05-05 01:14:17 2022-05-05 01:14:18 1.24 dict {'P08473': {CspaAnnotation(high_confidence=True, n_cell_types=29, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q92854': {CspaAnnotation(high_confidence=True, n_cell_types=26, tm=1, gpi=0, uniprot_cell_surface=True)}, 'Q93033': {CspaAnnotation(high_confidence=True, n_cell_types=6, tm=1, gpi=0, uniprot_...(truncated) 1,446 {} 2022-05-05 01:14:17
pypath.inputs.cspa.cspa_cell_type_annotations 2022-05-05 01:14:18 2022-05-05 01:14:20 1.63 dict {'A1A5B4': {CspaCellType(cell_type='CD4pCD25n_Tcells', value=18.59847), CspaCellType(cell_type='SUDHL6', value=16.57829), CspaCellType(cell_type='HDLM2', value=16.69533), CspaCellType(cell_type='A431', value=16.56885), CspaCellType(cell_type='NK', value=16.32343), CspaCellType(cell_type='HBL1', valu...(truncated) 1,407 {} 2022-05-05 01:14:18
pypath.inputs.cspa.cspa_cell_types 2022-05-05 01:14:20 2022-05-05 01:14:20 0.52 dict {'A431': {'A1A5B4': 16.56885, 'A1A5C7': None, 'A0A0B4J2A2': None, 'P0DN37': None, 'A2RU67': None, 'A2VDJ0': None, 'A6NGN9': None, 'A6NI73': None, 'A6NKL6': None, 'A6NMZ7': 16.08666, 'A7MBM2': 15.11804, 'A8MVW0': None, 'A8MVW5': None, 'A8MWY0': None, 'A8TX70': None, 'O00116': None, 'O00206': 15.9843,...(truncated) 47 {} 2022-05-05 01:14:20
pypath.inputs.cytosig.cytosig_annotations 2022-05-05 01:14:20 2022-05-05 01:14:42 21.19 dict {'Q9NPC4': {CytosigAnnotation(cytokine='P22301', score=-0.0353693407415396), CytosigAnnotation(cytokine='P10600', score=0.300776614000001), CytosigAnnotation(cytokine='O95390', score=0.1075145164614808), CytosigAnnotation(cytokine='P05231', score=0.0084669266516721), CytosigAnnotation(cytokine='P142...(truncated) 4,889 {} 2022-05-05 01:14:20
pypath.inputs.cytosig.cytosig_df 2022-05-05 01:14:42 2022-05-05 01:14:42 0.04 DataFrame Activin A BDNF BMP2 ... TWEAK VEGFA WNT3A A4GALT -0.135495 0.000000 -0.018502 ... 0.019689 -0.102361 0.013743 AAGAB 0.307167 0.074810 -0.070991 ... 0.077434 -0.009463 -0.005953 AAK1 -0.120398 -0.076692 -0.003144 ... -0.025428 0.020631 -0.045658 AAMDC ...(truncated) 4,881 {} 2022-05-05 01:14:42
pypath.inputs.dbptm.dbptm_enzyme_substrate 2022-05-05 01:14:42 2022-05-05 01:15:00 18.45 list [{'substrate': 'P30443', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end': 116, 'instance': 'TLRGYYNQSEDGS', 'typ': 'n-linked glycosylation', 'source': 'Swiss-Prot', 'references': ['19159218']}, {'substrate': 'P01892', 'kinase': None, 'resnum': 110, 'resaa': 'N', 'start': 104, 'end':...(truncated) 223,135 {} 2022-05-05 01:14:42
pypath.inputs.dbptm.dbptm_enzyme_substrate_old 2022-05-05 01:15:01 2022-05-05 01:15:05 4.67 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/dbptm.py", line 102, in dbptm_enzyme_substrate_old
    for k, data in iteritems(extra):
  File "/usr/lib/python3/dist-packages/future/utils/__init__.py", line 311, in iteritems
    func = obj.items
AttributeError: 'NoneType' object has no attribute 'items'
{} 2022-01-07 23:35:25
pypath.inputs.dbptm.dbptm_interactions 2022-05-05 01:15:05 2022-05-05 01:15:07 1.30 list [['PKA', 'P63104', '11956222;12865427;15883165;16376338'], ['PKB', 'P63104', '11956222;12865427;15883165;16376338'], ['MAPK8', 'P63104', '15071501;15696159'], ['CDK1', 'P11171', '2171679;15525677;18220336;18669648'], ['MAPK1', 'Q13541', '12747827;17081983;17287340;18187866;18669648'], ['CK2', 'P0506...(truncated) 2,071 {} 2022-05-05 01:15:05
pypath.inputs.deathdomain.deathdomain_interactions 2022-05-05 01:15:07 2022-05-05 01:15:08 1.16 list [] 0 {} 2022-05-05 01:15:07
pypath.inputs.deathdomain.deathdomain_interactions_rescued 2022-05-05 01:15:08 2022-05-05 01:15:08 0.15 list [['Apaf1', 'Caspase9', 'GST fusion protein pull-down;In vitro purification protein assembly(Size-exclusion chromatography);Yeast two-hybrid;Co-immunoprecipitation;Size-exclusion chromatography;Structure;Gel filtration;β-galactosidase staining;DAPI staining;Caspase cleaved assay', '9390557;9922454;11...(truncated) 184 {} 2022-05-05 01:15:08
pypath.inputs.depod.depod_enzyme_substrate 2022-05-05 01:15:08 2022-05-05 01:15:08 0.10 list [{'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1054, 'references': ['11201744'], 'substrate': 'P29597', 'start': None, 'end': None, 'typ': 'dephosphorylation'}, {'instance': None, 'kinase': 'P08575', 'resaa': 'Y', 'resnum': 1055, 'references': ['11201744'], 'substrate': 'P29597', 's...(truncated) 537 {} 2022-05-05 01:15:08
pypath.inputs.depod.depod_interactions 2022-05-05 01:15:08 2022-05-05 01:15:08 0.01 list [('P15309', 'P04626', '11067847|9705354', '2', 'dephosphorylation reaction'), ('Q9BZG2', 'Q15303', '15219672', '1', 'dephosphorylation reaction'), ('P05186', 'P0C0S8', '6167574', '1', 'dephosphorylation reaction'), ('P05186', 'Q92934', 'PMC3005908', '1', 'dephosphorylation reaction'), ('P49593', 'Q1...(truncated) 832 {} 2022-05-05 01:15:08
pypath.inputs.dgidb.dgidb_annotations 2022-05-05 01:15:08 2022-05-05 01:15:11 3.08 dict {'Q9BXS1': {DgidbAnnotation(category='ENZYME')}, 'Q9BZH6': {DgidbAnnotation(category='TRANSCRIPTION FACTOR')}, 'Q96Q89': {DgidbAnnotation(category='ENZYME')}, 'Q99470': {DgidbAnnotation(category='DRUGGABLE GENOME')}, 'Q9H211': {DgidbAnnotation(category='KINASE')}, 'O95069': {DgidbAnnotation(category...(truncated) 10,493 {} 2022-05-05 01:15:08
pypath.inputs.dgidb.get_dgidb_old 2022-05-05 01:15:11 2022-05-05 01:16:24 72.71 set {'Q08828', 'P19525', 'P12524', 'O14733', 'P51589', 'Q14289', 'Q15077', 'P07384', 'O43306', 'Q8NGR3', 'P05412', 'Q9UPI3', 'P21941', 'Q96NZ8', 'P08174', 'P45984', 'Q08345', 'Q99712', 'P43250', 'Q96FZ2', 'Q8TF68', 'Q9H3N8', 'Q9H3D4', 'Q5XLA6', 'Q9UHX3', 'P04234', 'P15173', 'P12830', 'Q13490', 'Q06481',...(truncated) 5,900 {} 2022-05-05 01:15:11
pypath.inputs.dip.dip_interactions 2022-05-05 01:16:24 2022-05-05 01:16:24 0.45 list [['P01730', 'P01730', '9168119;9168119', 'direct interaction', 'x-ray crystallography;protein cross-linking with a bifunctional reagent', 'DIP-42E'], ['P29375', 'P06400', '8414517;22615382;22615382', 'physical interaction;physical association', 'biochemical;anti bait coimmunoprecipitation', 'DIP-214...(truncated) 2,283 {} 2022-05-05 01:16:24
pypath.inputs.dip.dip_login 
Not calling `pypath.inputs.dip.dip_login`, not enough arguments.
 {} never
pypath.inputs.disgenet.disgenet_annotations 2022-05-05 01:16:24 2022-05-05 01:16:35 10.50 dict {'P04217': {DisGeNetAnnotation(disease='Hepatomegaly', type='phenotype', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',)), DisGeNetAnnotation(disease='Schizophrenia', type='disease', score=0.3, dsi=0.7, dpi=0.538, nof_pmids=1, nof_snps=0, source=('CTD_human',))}, 'P0102...(truncated) 9,203 {} 2022-05-05 01:16:24
pypath.inputs.domino.domino_ddi 2022-05-05 01:16:35 2022-05-05 01:16:46 11.07 list [<pypath.internals.intera.DomainDomain object at 0x7f2d4759f5e0>, <pypath.internals.intera.DomainDomain object at 0x7f2d4759e410>, <pypath.internals.intera.DomainDomain object at 0x7f2d4759edd0>, <pypath.internals.intera.DomainDomain object at 0x7f2d4759f400>, <pypath.internals.intera.DomainDomain o...(truncated) 1,294 {} 2022-05-05 01:16:35
pypath.inputs.domino.domino_enzsub 2022-05-05 01:16:46 2022-05-05 01:16:47 0.94 dict {'ddi': [<pypath.internals.intera.DomainDomain object at 0x7f2d404bcd90>, <pypath.internals.intera.DomainDomain object at 0x7f2d404bfd90>, <pypath.internals.intera.DomainDomain object at 0x7f2d404bceb0>, <pypath.internals.intera.DomainDomain object at 0x7f2d404bd120>, <pypath.internals.intera.Domain...(truncated) 2 {} 2022-05-05 01:16:46
pypath.inputs.domino.domino_interactions 2022-05-05 01:16:47 2022-05-05 01:16:47 0.37 list [DominoRecord(uniprot_A='A4GZ26', uniprot_B='Q8BKX1', isoform_A='1', isoform_B='1', exp_method='two hybrid', references='10.1016/j.brainres.2008.11.061', taxon_A='10090', taxon_B='10090', role_A='physical association', role_B='unspecified role', binding_site_range_A='1424-1434', binding_site_range_B...(truncated) 6,687 {} 2022-05-05 01:16:47
pypath.inputs.domino.get_domino 2022-05-05 01:16:47 2022-05-05 01:16:48 0.36 list [DominoRecord(uniprot_A='O00459', uniprot_B='', isoform_A='1', isoform_B='', exp_method='', references='', taxon_A='9606', taxon_B='', role_A='mint', role_B='neutral component', binding_site_range_A='4-80', binding_site_range_B='', domains_A='', domains_B='', ptm_residue_A='', ptm_residue_B='', ptm_...(truncated) 14,539 {} 2022-05-05 01:16:47
pypath.inputs.dorothea._process_resources 
Not calling `pypath.inputs.dorothea._process_resources`, not enough arguments.
 {} never
pypath.inputs.dorothea.dorothea_full_raw 2022-05-05 01:16:48 2022-05-05 01:16:56 7.85 DataFrame tf target mor ... which_inferred which_tfbs pubmed_id 0 ADNP AASDH 0.0 ... gtex none - 1 ADNP AASDHPPT 0.0 ... gtex none - 2 ADNP ABCB10 0.0 ... gtex none - 3 ADN...(truncated) 1,019,220 {} 2022-05-05 01:16:48
pypath.inputs.dorothea.dorothea_interactions 2022-05-05 01:16:56 2022-05-05 01:17:08 12.68 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2022-05-05 01:16:56
pypath.inputs.dorothea.dorothea_old_csv 2022-05-05 01:17:08 2022-05-05 01:17:09 0.48 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.dorothea.dorothea_old_csv 2022-05-05 01:17:09 2022-05-05 01:17:09 0.40 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.dorothea.dorothea_rda_raw 2022-05-05 01:17:09 2022-05-05 01:17:11 1.96 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2022-05-05 01:17:09
pypath.inputs.dorothea.get_dorothea_old 2022-05-05 01:17:11 2022-05-05 01:17:12 0.81 list [['AHR', 'CYP1A1', '0', 'A', True, False, True, False, 'HTRIdb,trrust_signed', '', 'hocomoco_v11', '', 'HTRIdb,trrust_signed,hocomoco_v11'], ['AHR', 'CYP1A2', '0', 'A', True, False, False, False, 'HTRIdb,trrust_signed', '', '', '', 'HTRIdb,trrust_signed'], ['AHR', 'CYP1B1', '0', 'A', True, False, Tr...(truncated) 14,260 {} 2022-05-05 01:17:11
pypath.inputs.dorothea.dorothea_rda_raw 2022-05-05 01:17:12 2022-05-05 01:17:13 1.12 DataFrame tf confidence target mor 0 ADNP D ATF7IP 1.0 1 ADNP D DYRK1A 1.0 2 ADNP D TLK1 1.0 3 ADNP D ZMYM4 1.0 4 ADNP D ABCC1 1.0 ... ... ... ... ... 454499 ZZZ3 D ZBTB20 1.0 4545...(truncated) 454,504 {} 2022-05-05 01:17:12
pypath.inputs.dorothea.dorothea_interactions 2022-05-05 01:17:13 2022-05-05 01:17:26 12.67 list [DorotheaInteraction(tf='ADNP', target='ABCC1', effect=0, level='D', curated=False, chipseq=True, predicted=False, coexp=False, curated_sources='', chipseq_sources='ReMap', predicted_sources='', coexp_sources='', all_sources='ReMap', pubmed='', kegg_pathways=''), DorotheaInteraction(tf='ADNP', targe...(truncated) 309,009 {} 2022-05-05 01:17:13
pypath.inputs.dorothea.dorothea_old_csv 2022-05-05 01:17:26 2022-05-05 01:17:26 0.26 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/dorothea.py", line 214, in dorothea_old_csv
    reader = csv.DictReader(c.result['database.csv'])
TypeError: 'NoneType' object is not subscriptable
{} 2022-01-07 23:37:25
pypath.inputs.ebi.ebi_rest 
Not calling `pypath.inputs.ebi.ebi_rest`, not enough arguments.
 {} never
pypath.inputs.elm.elm_classes 2022-05-05 01:17:26 2022-05-05 01:17:26 0.13 dict {'CLV_C14_Caspase3-7': ELMClass(accession='ELME000321', identifier='CLV_C14_Caspase3-7', functional_name='Caspase cleavage motif', description='Caspase-3 and Caspase-7 cleavage site.', regex='[DSTE][^P][^DEWHFYC]D[GSAN]', probability='0.00309374033071', n_instances='41', n_pdb='0'), 'CLV_MEL_PAP_1':...(truncated) 317 {} 2022-05-05 01:17:26
pypath.inputs.elm.elm_domains 2022-05-05 01:17:26 2022-05-05 01:17:27 0.49 dict {'FZR_HUMAN': {'LIG_APCC_Dbox_1': [('218', '471')]}, 'BIRC3_HUMAN': {'LIG_BIR_II_1': [('172', '236')]}} 2 {} 2022-05-05 01:17:26
pypath.inputs.elm.elm_instances 2022-05-05 01:17:27 2022-05-05 01:17:27 0.45 list [ELMInstance(accession='ELMI003774', type='CLV', identifier='CLV_C14_Caspase3-7', uniprot_id='A0A0H3NIK3_SALTS', uniprot='A0A0H3NIK3', synonyms='A0A0H3NIK3', start='483', end='487', references='20947770', methods='enzymatic reaction; mutation analysis; protease assay; western blot', logic='true posi...(truncated) 3,934 {} 2022-05-05 01:17:27
pypath.inputs.elm.elm_interactions 2022-05-05 01:17:27 2022-05-05 01:17:28 0.18 list [ELMInteraction(motif_elm='CLV_Separin_Fungi', domain_pfam='PF03568', uniprot_motif='Q12158', uniprot_domain='Q03018', isoform_motif=1, isoform_domain=1, start_motif=175, end_motif=181, start_domain=1171, end_domain=1571, affinity_min=None, affinity_max=None, pubmeds=(10403247, 14585836), taxon_moti...(truncated) 2,394 {} 2022-05-05 01:17:27
pypath.inputs.embopress.embopress_supplementary 
Not calling `pypath.inputs.embopress.embopress_supplementary`, not enough arguments.
 {} never
pypath.inputs.embrace._embrace_id_translation 
Not calling `pypath.inputs.embrace._embrace_id_translation`, not enough arguments.
 {} never
pypath.inputs.embrace.embrace_annotations 2022-05-05 01:17:28 2022-05-05 01:19:30 122.16 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 163, in embrace_annotations
    for rec in embrace_translated(organism = organism):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 93, in embrace_translated
    ligands = _embrace_id_translation(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
    uniprots = homology.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 1187, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 258, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 172, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 203, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 213, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 485, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 501, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 640, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 94, in homologene_dict
    for l in hg:
TypeError: 'NoneType' object is not iterable
{} 2022-05-01 01:20:57
pypath.inputs.embrace.embrace_interactions 2022-05-05 01:19:30 2022-05-05 01:20:33 63.39 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 129, in embrace_interactions
    for rec in embrace_translated(organism = organism)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 93, in embrace_translated
    ligands = _embrace_id_translation(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
    uniprots = homology.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 1187, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 258, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 172, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 203, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 213, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 485, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 501, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 640, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 105, in homologene_dict
    this_taxon = int(l[1].strip())
IndexError: list index out of range
{} 2022-05-01 01:32:42
pypath.inputs.embrace.embrace_raw 2022-05-05 01:20:33 2022-05-05 01:20:33 0.10 list [EmbraceRawRecord(ligand_symbol='A2m', receptor_symbol='Lrp1', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=0, N_receptor=1, P_receptor=0, M_receptor=1, EC_receptor=0), EmbraceRawRecord(ligand_symbol='Ace', receptor_symbol='Bdkrb2', N_ligand=1, P_ligand=0, M_ligand=0, EC_ligand=1, N_receptor=0, P_r...(truncated) 1,710 {} 2022-05-05 01:20:33
pypath.inputs.embrace.embrace_translated 2022-05-05 01:20:33 2022-05-05 01:20:34 0.63 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 93, in embrace_translated
    ligands = _embrace_id_translation(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/embrace.py", line 72, in _embrace_id_translation
    uniprots = homology.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 1187, in translate
    return manager.translate(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 258, in translate
    table = self.which_table(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 172, in which_table
    self.load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 203, in load
    self.tables[key] = self._load(key)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 213, in _load
    return ProteinHomology(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 485, in __init__
    self.load(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 501, in load
    self.load_homologene(source)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/homology.py", line 640, in load_homologene
    hge = homologene_input.homologene_dict(source, self.target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 105, in homologene_dict
    this_taxon = int(l[1].strip())
IndexError: list index out of range
{} 2022-05-01 01:32:43
pypath.inputs.encode.encode_tf_mirna_interactions 2022-05-05 01:20:34 2022-05-05 01:20:35 0.73 list [EncodeInteraction(tf_genesymbol='BDP1', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='RAD21', mirna='hsa-miR-92a-1*'), EncodeInteraction(tf_genesymbol='ESR1', mirna='hsa-miR-23b*'), EncodeInteraction(tf_genesymbol='BCL3', mirna='hsa-miR-19b-1*'), EncodeInteraction(tf_genesymbol='HEY1', ...(truncated) 1,237 {} 2022-05-05 01:20:34
pypath.inputs.ensembl.ensembl_organisms 2022-05-05 01:20:35 2022-05-05 01:20:35 0.72 list [EnsemblOrganism(common_name='Abingdon island giant tortoise', scientific_name='Chelonoidis abingdonii', taxon_id=106734, ensembl_assembly='ASM359739v1', accession='GCA_003597395.1', genebuild_method='Full genebuild', variation_database='-', regulation_database='-', ensembl_name='cabingdonii'), Ense...(truncated) 311 {} 2022-05-05 01:20:35
pypath.inputs.exocarta._get_exocarta_vesiclepedia 2022-05-05 01:20:35 2022-05-05 01:20:54 18.48 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2022-05-05 01:20:35
pypath.inputs.exocarta.get_exocarta 2022-05-05 01:20:54 2022-05-05 01:20:54 0.03 list [('967', 'CD63', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('1803', 'DPP4', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('79574', 'EPS8L3', 9606, ('11487543', (9606,), 'Intestinal epithelial cells')), ('55971', 'BAIAP2L1', 9606, ('11487543', (9606,), 'Intestinal e...(truncated) 32,085 {} 2022-05-05 01:20:54
pypath.inputs.exocarta.get_vesiclepedia 2022-05-05 01:20:54 2022-05-05 01:21:58 64.30 list [('31848', 'His3.3B', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('33736', 'His3.3A', 9606, ('16342139', (9606,), 'B cells', ('Microparticles',))), ('1', 'A1BG', 9606, ('19056867', (9606,), 'Urine', ('Exosomes',))), ('1', 'A1BG', 9606, ('21630462', (9606,), 'Ascites', ('Microvesic...(truncated) 290,197 {} 2022-05-05 01:20:54
pypath.inputs.genecards.genecards_datasheet 
Not calling `pypath.inputs.genecards.genecards_datasheet`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_soup 
Not calling `pypath.inputs.genecards.genecards_soup`, not enough arguments.
 {} never
pypath.inputs.genecards.genecards_summaries 
Not calling `pypath.inputs.genecards.genecards_summaries`, not enough arguments.
 {} never
pypath.inputs.go.get_go_desc 
Not calling `pypath.inputs.go.get_go_desc`, not enough arguments.
 {} never
pypath.inputs.go.get_go_quick 2022-05-05 01:21:58 2022-05-05 01:21:58 0.36 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 861, in get_go_quick
    _ = next(c.result)
TypeError: 'NoneType' object is not an iterator
{} 2022-01-07 23:44:17
pypath.inputs.go.get_goslim 2022-05-05 01:21:58 2022-05-05 01:21:59 0.91 list ['GO:0000228', 'GO:0000278', 'GO:0000910', 'GO:0002181', 'GO:0002376', 'GO:0003012', 'GO:0003013', 'GO:0003014', 'GO:0003016', 'GO:0003677', 'GO:0003723', 'GO:0003774', 'GO:0003924', 'GO:0005198', 'GO:0005215', 'GO:0005576', 'GO:0005615', 'GO:0005618', 'GO:0005634', 'GO:0005635', 'GO:0005654', 'GO:0...(truncated) 141 {} 2022-05-05 01:21:58
pypath.inputs.go.go_ancestors_quickgo 2022-05-05 01:21:59 2022-05-05 01:37:22 922.70 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016014': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016011': {('GO:0098797', 'is_a'), ...(truncated) 3 {} 2022-05-05 01:21:59
pypath.inputs.go.go_ancestors_goose 2022-05-05 01:37:22 2022-05-05 01:37:27 4.97 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 146, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:57:44
pypath.inputs.go.go_ancestors_quickgo 2022-05-05 01:37:27 2022-05-05 01:37:31 3.83 dict {'C': {'GO:0016006': {('GO:0016007', 'is_a')}, 'GO:0016008': {('GO:0016007', 'is_a')}, 'GO:0016009': {('GO:0016007', 'is_a')}, 'GO:0016014': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016013': {('GO:0098797', 'is_a'), ('GO:0016010', 'part_of')}, 'GO:0016011': {('GO:0098797', 'is_a'), ...(truncated) 3 {} 2022-05-05 01:37:27
pypath.inputs.go.go_annotations_goa 2022-05-05 01:37:31 2022-05-05 01:37:37 5.95 dict {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) 3 {} 2022-05-05 01:37:31
pypath.inputs.go.go_annotations_goa 2022-05-05 01:37:37 2022-05-05 01:37:38 0.98 dict {'C': {'A0A024RBG1': {'GO:0005634', 'GO:0005737', 'GO:0005829'}, 'A0A075B6H5': {'GO:0005886'}, 'A0A075B6H7': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6H8': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6H9': {'GO:0005886', 'GO:0005615', 'GO:0019814'}, 'A0A075B6I0': {'GO:0005886', 'G...(truncated) 3 {} 2022-05-05 01:37:37
pypath.inputs.go.go_annotations_goose 2022-05-05 01:37:38 2022-05-05 01:37:41 3.26 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 796, in go_annotations_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:57:55
pypath.inputs.go.go_annotations_solr 2022-05-05 01:37:41 2022-05-05 01:37:42 1.14 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 682, in go_annotations_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2022-01-07 23:57:58
pypath.inputs.go.go_annotations_uniprot 2022-05-05 01:37:42 2022-05-05 01:37:49 6.30 dict {'Entry': ['Gene ontology IDs'], 'P51451': ['GO:0002431', 'GO:0002513', 'GO:0002576', 'GO:0002902', 'GO:0004712', 'GO:0004713', 'GO:0004715', 'GO:0005102', 'GO:0005524', 'GO:0005829', 'GO:0006974', 'GO:0007169', 'GO:0018108', 'GO:0030154', 'GO:0030889', 'GO:0031175', 'GO:0031234', 'GO:0032024', 'GO:...(truncated) 20,377 {} 2022-05-05 01:37:42
pypath.inputs.go.go_descendants_quickgo 2022-05-05 01:37:49 2022-05-05 01:37:53 3.73 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016008', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016014', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016011', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0031617': {('GO:0031262', 'part_of...(truncated) 3 {} 2022-05-05 01:37:49
pypath.inputs.go.go_descendants_goose 2022-05-05 01:37:53 2022-05-05 01:37:56 3.32 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 223, in go_descendants_goose
    anc = go_ancestors_goose(aspects = aspects)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 146, in go_ancestors_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:58:11
pypath.inputs.go.go_descendants_quickgo 2022-05-05 01:37:56 2022-05-05 01:38:00 3.72 dict {'C': defaultdict(<class 'set'>, {'GO:0016007': {('GO:0016006', 'is_a'), ('GO:0016008', 'is_a'), ('GO:0016009', 'is_a')}, 'GO:0016010': {('GO:0016014', 'part_of'), ('GO:0016013', 'part_of'), ('GO:0016011', 'part_of')}, 'GO:0016011': {('GO:0016012', 'part_of')}, 'GO:0031617': {('GO:0031262', 'part_of...(truncated) 3 {} 2022-05-05 01:37:56
pypath.inputs.go.go_descendants_to_ancestors 
Not calling `pypath.inputs.go.go_descendants_to_ancestors`, not enough arguments.
 {} never
pypath.inputs.go.go_terms_quickgo 2022-05-05 01:38:00 2022-05-05 01:38:03 3.04 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2022-05-05 01:38:00
pypath.inputs.go.go_terms_goose 2022-05-05 01:38:03 2022-05-05 01:38:06 3.36 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 520, in go_terms_goose
    for l in c.result:
TypeError: 'NoneType' object is not iterable
{} 2022-01-07 23:58:20
pypath.inputs.go.go_terms_quickgo 2022-05-05 01:38:06 2022-05-05 01:38:09 3.07 dict {'C': {'GO:0016007': 'mitochondrial derivative', 'GO:0043626': 'PCNA complex', 'GO:0016008': 'major mitochondrial derivative', 'GO:0043625': 'delta DNA polymerase complex', 'GO:0016009': 'minor mitochondrial derivative', 'GO:0016010': 'dystrophin-associated glycoprotein complex', 'GO:0016011': 'dyst...(truncated) 3 {} 2022-05-05 01:38:06
pypath.inputs.go.go_terms_solr 2022-05-05 01:38:09 2022-05-05 01:38:10 0.60 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/go.py", line 378, in go_terms_solr
    parser = etree.iterparse(c.fileobj, events = ('start', 'end'))
AttributeError: 'Curl' object has no attribute 'fileobj'
{} 2022-01-07 23:58:26
pypath.inputs.gpcrdb.gpcrdb_annotations 2022-05-05 01:38:10 2022-05-05 01:38:10 0.26 dict {'P08908': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28222': {GpcrdbAnnotation(gpcr_class='Class A (Rhodopsin)', family='Aminergic receptors', subfamily='5-Hydroxytryptamine receptors')}, 'P28221': {GpcrdbAnnotati...(truncated) 402 {} 2022-05-05 01:38:10
pypath.inputs.graphviz.graphviz_attrs 2022-05-05 01:38:10 2022-05-05 01:38:11 1.06 tuple ({'_background': {'type': 'string', 'default': '<none>', 'min': '', 'notes': ''}, 'bb': {'type': 'rect', 'default': '', 'min': '', 'notes': 'write only'}, 'bgcolor': {'type': 'colorcolorList', 'default': '<none>', 'min': '', 'notes': ''}, 'center': {'type': 'bool', 'default': 'false', 'min': '', 'no...(truncated) 3 {} 2022-05-05 01:38:10
pypath.inputs.guide2pharma.guide2pharma_complexes 
Not calling `pypath.inputs.guide2pharma.guide2pharma_complexes`, not enough arguments.
 {} never
pypath.inputs.guide2pharma.guide2pharma_download 2022-05-05 01:38:11 2022-05-05 01:38:19 8.11 tuple ([GuideToPharmacologyInteraction(ligand='TNFSF9', ligand_id_type='genesymbol', target='Q07011', target_id_type='uniprot', target_is_ligand=False, ligand_organism=9606, target_organism=9606, effect=0, ligand_location=None, target_type=None, ligand_endogenous=True, pubmed_ids=[]), GuideToPharmacologyI...(truncated) 2 {} 2022-05-05 01:38:11
pypath.inputs.guide2pharma.guide2pharma_interactions 
Not calling `pypath.inputs.guide2pharma.guide2pharma_interactions`, not enough arguments.
 {} never
pypath.inputs.havugimana.get_havugimana 2022-05-05 01:38:19 2022-05-05 01:38:21 1.75 list [['C_1', '2.0', 'O60547,P30043', 'GMDS_HUMAN,BLVRB_HUMAN', '0.0', 'O60547,P30043,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'Fungi'], ['C_2', '2.0', 'Q92785,Q9NVP1', 'REQU_HUMAN,DDX18_HUMAN', '0.0', 'Q92785,Q9NVP1,', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'vertebrates'], ['C_3', '2.0', 'Q...(truncated) 622 {} 2022-05-05 01:38:19
pypath.inputs.havugimana.havugimana_complexes 2022-05-05 01:38:21 2022-05-05 01:38:21 0.03 dict {'COMPLEX:O60547_P30043': Complex: COMPLEX:O60547_P30043, 'COMPLEX:Q92785_Q9NVP1': Complex: COMPLEX:Q92785_Q9NVP1, 'COMPLEX:O95249_Q86Y82': Complex: COMPLEX:O95249_Q86Y82, 'COMPLEX:P26583_Q9UPN6': Complex: COMPLEX:P26583_Q9UPN6, 'COMPLEX:P15408_P18846': Complex: COMPLEX:P15408_P18846, 'COMPLEX:P2325...(truncated) 622 {} 2022-05-05 01:38:21
pypath.inputs.hgnc.hgnc_genegroups 2022-05-05 01:38:21 2022-05-05 01:38:31 9.61 dict {'P04217': {HGNCGeneGroupAnnotation(mainclass='Immunoglobulin like domain containing')}, 'Q9NQ94': {HGNCGeneGroupAnnotation(mainclass='RNA binding motif containing')}, 'P01023': {HGNCGeneGroupAnnotation(mainclass='C3 and PZP like, alpha-2-macroglobulin domain containing')}, 'A8K2U0': {HGNCGeneGroupA...(truncated) 15,003 {} 2022-05-05 01:38:21
pypath.inputs.hippie.hippie_interactions 2022-05-05 01:38:31 2022-05-05 01:39:17 46.63 list [HippieInteraction(id_a='O94952', id_b='Q9Y6B2', score=0.89, methods=None, references=('26085330', '26631746', '28514442', '33961781'), sources=None, organisms=None), HippieInteraction(id_a='Q9H9A6', id_b='P07205', score=0.82, methods=None, references=('28514442', '33961781'), sources=None, organism...(truncated) 102,256 {} 2022-05-05 01:38:31
pypath.inputs.homologene.get_homologene 2022-05-05 01:39:17 2022-05-05 01:39:18 0.11 list ['3\t9606\t34\tACADM\t4557231\tNP_000007.1\n', '3\t9598\t469356\tACADM\t160961497\tNP_001104286.1\n', '3\t9544\t705168\tACADM\t109008502\tXP_001101274.1\n', '3\t9615\t490207\tACADM\t545503811\tXP_005622188.1\n', '3\t9913\t505968\tACADM\t115497690\tNP_001068703.1\n', '3\t10090\t11364\tAcadm\t6680618\...(truncated) 839,297 {'size': 561158} 2022-05-05 01:39:17
pypath.inputs.homologene.homologene_dict 
Not calling `pypath.inputs.homologene.homologene_dict`, not enough arguments.
 {} never
pypath.inputs.homologene.homologene_uniprot_dict 
Not calling `pypath.inputs.homologene.homologene_uniprot_dict`, not enough arguments.
 {} never
pypath.inputs.hpmr.get_hpmr 2022-05-05 01:39:18 2022-05-05 01:39:18 0.00 dict {'interactions': [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462...(truncated) 3 {} 2022-05-05 01:39:18
pypath.inputs.hpmr.hpmr_annotations 2022-05-05 01:39:18 2022-05-05 01:39:18 0.00 dict {'P26992': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='CICYTR (Cytokine Type 1 receptors)', subsubclass=None)}, 'P40189': {HPMRAnnotation(role='Receptor', mainclass='Cytokine Type 1 receptors', subclass='OSMR(Cytokine Type 1 receptors)', subsubclass=None)}, 'P42...(truncated) 1,141 {} 2022-05-05 01:39:18
pypath.inputs.hpmr.hpmr_complexes 2022-05-05 01:39:18 2022-05-05 01:39:18 0.00 dict {} 0 {} 2022-05-05 01:39:18
pypath.inputs.hpmr.hpmr_interactions 2022-05-05 01:39:18 2022-05-05 01:39:18 0.00 list [['P26992', 'Receptor', 'P40189', '15051883'], ['P26992', 'Receptor', 'P42702', '15051883'], ['P26992', 'Ligand', 'P00491', '15051883'], ['O75462', 'Receptor', 'P26992', '10966616'], ['O75462', 'Receptor', 'P40189', '10966616'], ['O75462', 'Receptor', 'P42702', '10966616'], ['O75462', 'Ligand', 'P26...(truncated) 619 {} 2022-05-05 01:39:18
pypath.inputs.hprd.get_hprd 2022-05-05 01:39:18 2022-05-05 01:39:46 28.43 list [['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '128', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '91', 'K', '-', '-', 'Acetylation', 'in vivo', '19608861'], ['00001', 'ALDH1A1', '00001_1', 'NP_000680.2', '353', 'K', '-', '-', 'Acetylation', ...(truncated) 86,981 {} 2022-05-05 01:39:18
pypath.inputs.hprd.hprd_enzyme_substrate 2022-05-05 01:39:46 2022-05-05 01:39:48 1.54 list [{'resaa': 'Y', 'resnum': 12, 'typ': 'dephosphorylation', 'references': ['16291744'], 'kinase': 'PTPN1', 'substrate_refseqp': 'NP_001093.1', 'substrate': 'ACTN1', 'start': 5, 'end': 19, 'instance': None}, {'resaa': 'Y', 'resnum': 705, 'typ': 'phosphorylation', 'references': ['11940572', '11294897', ...(truncated) 4,671 {} 2022-05-05 01:39:46
pypath.inputs.hprd.hprd_interactions 2022-05-05 01:39:48 2022-05-05 01:39:49 1.52 list [['00020', 'ACTN1', '00020_1', 'NP_001093.1', '12', 'Y', 'PTPN1', '01477', 'Dephosphorylation', 'in vitro;in vivo', '16291744'], ['00026', 'STAT3', '00026_1', 'NP_644805.1', '705', 'Y', 'FGFR3', '00624', 'Phosphorylation', 'in vivo', '11940572,11294897,10918587,12244095,11350938,12626508,8626374,125...(truncated) 4,671 {} 2022-05-05 01:39:48
pypath.inputs.hprd.hprd_interactions_htp 2022-05-05 01:39:49 2022-05-05 01:39:50 1.29 list [['ALDH1A1', '00001', 'NP_000680.2', 'ALDH1A1', '00001', 'NP_000680.2', 'in vivo;yeast 2-hybrid', '12081471,16189514'], ['ITGA7', '02761', 'NP_001138468.1', 'CHRNA1', '00007', 'NP_001034612.1', 'in vivo', '10910772'], ['PPP1R9A', '16000', 'NP_060120.2', 'ACTG1', '00017', 'NP_001605.1', 'in vitro;in ...(truncated) 39,241 {} 2022-05-05 01:39:49
pypath.inputs.htri.htri_interactions 2022-05-05 01:39:51 2022-05-05 01:39:54 3.60 list [HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='142', genesymbol_tf='PARP1', entrez_target='675', genesymbol_target='BRCA2', pubmed='18990703'), HTRIInteraction(entrez_tf='196', genesymbol_tf='AHR...(truncated) 18,630 {} 2022-05-05 01:39:51
pypath.inputs.humancellmap.humancellmap_annotations 2022-05-05 01:39:54 2022-05-05 01:39:57 2.38 dict {'Q9NRG9': {HumancellmapAnnotation(localization='mitochondrial outer membrane', method='NMF'), HumancellmapAnnotation(localization='nuclear outer membrane-ER membrane network', method='SAFE'), HumancellmapAnnotation(localization='peroxisome', method='NMF')}, 'Q2M2I8': {HumancellmapAnnotation(localiz...(truncated) 4,371 {} 2022-05-05 01:39:54
pypath.inputs.humap.humap2_complexes 2022-05-05 01:39:57 2022-05-05 01:40:00 3.73 dict {'COMPLEX:O95900_Q9BQS8': Complex: COMPLEX:O95900_Q9BQS8, 'COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9': Complex: COMPLEX:P08133_P68402_Q15102_Q15797_Q99426_Q9H4M9, 'COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6ZRY4_Q93062_Q96S66_Q9NZC3_Q9UF11_Q9Y6M7': Complex: COMPLEX:A1KXE4_O43251_Q15038_Q15434_Q6Z...(truncated) 6,942 {} 2022-05-05 01:39:57
pypath.inputs.humap.humap_complexes 2022-05-05 01:40:00 2022-05-05 01:40:02 1.77 dict {'COMPLEX:Q7L523_Q8NBW4_Q9HB90': Complex: COMPLEX:Q7L523_Q8NBW4_Q9HB90, 'COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3': Complex: COMPLEX:O75478_O75528_Q8IYH5_Q92830_Q92831_Q9H8E8_Q9ULM3, 'COMPLEX:P31942_Q32P51': Complex: COMPLEX:P31942_Q32P51, 'COMPLEX:P35606_Q9NTJ5_Q9UBF2': Complex: COM...(truncated) 4,499 {} 2022-05-05 01:40:00
pypath.inputs.huri._huri_interactions 
Not calling `pypath.inputs.huri._huri_interactions`, not enough arguments.
 {} never
pypath.inputs.huri.hi_i_interactions 2022-05-05 01:40:02 2022-05-05 01:40:05 3.35 list [HuriInteraction(uniprot_a='Q8IY31', uniprot_b='Q9BQD3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='P49902', uniprot_b='P49902', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9BVJ6', uniprot_b='Q8NHQ1', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 5,676 {} 2022-05-05 01:40:02
pypath.inputs.huri.hi_ii_interactions 2022-05-05 01:40:05 2022-05-05 01:40:47 41.31 list [HuriInteraction(uniprot_a='Q9H2A7', uniprot_b='Q6UY14', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q5SY16', uniprot_b='Q09666', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P59797', uniprot_b='Q8NF64', isoform_a=1, isoform_b=3, score=None), HuriInteractio...(truncated) 46,898 {} 2022-05-05 01:40:05
pypath.inputs.huri.hi_iii_old 2022-05-05 01:40:47 2022-05-05 01:40:47 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/huri.py", line 95, in hi_iii_old
    url = urls.urls['hid']['hi-iii']
KeyError: 'hi-iii'
{} 2022-01-08 00:02:33
pypath.inputs.huri.hi_union_interactions 2022-05-05 01:40:47 2022-05-05 01:46:47 360.03 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/huri.py", line 303, in _huri_interactions
    c = curl.FileOpener(path)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 593, in __init__
    self.extract()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 623, in extract
    getattr(self, 'open_%s' % self.type)()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 740, in open_plain
    self._log('Opening plain text file `%s`.' % self.fileobj.name)
AttributeError: 'NoneType' object has no attribute 'name'
{} 2022-04-01 01:00:17
pypath.inputs.huri.huri_interactions 2022-05-05 01:46:47 2022-05-05 01:52:47 360.02 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/huri.py", line 303, in _huri_interactions
    c = curl.FileOpener(path)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 593, in __init__
    self.extract()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 623, in extract
    getattr(self, 'open_%s' % self.type)()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 740, in open_plain
    self._log('Opening plain text file `%s`.' % self.fileobj.name)
AttributeError: 'NoneType' object has no attribute 'name'
{} 2022-04-01 01:01:43
pypath.inputs.huri.lit_bm_13_interactions 2022-05-05 01:52:47 2022-05-05 01:52:49 1.77 list [LitBm13Interaction(entrez_a='4790', entrez_b='79155', genesymbol_a='NFKB1', genesymbol_b='TNIP2'), LitBm13Interaction(entrez_a='7879', entrez_b='83547', genesymbol_a='RAB7A', genesymbol_b='RILP'), LitBm13Interaction(entrez_a='3932', entrez_b='80306', genesymbol_a='LCK', genesymbol_b='MED28'), LitBm...(truncated) 11,045 {} 2022-05-05 01:52:47
pypath.inputs.huri.lit_bm_17_interactions 2022-05-05 01:52:49 2022-05-05 01:53:00 11.44 list [LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18789323', score=0.659), LitBm17Interaction(id_a='P07359', id_b='P13224', pubmed='18674540', score=0.659), LitBm17Interaction(id_a='P63104', id_b='P13224', pubmed='10627461', score=0.702), LitBm17Interaction(id_a='P63104', id_b='P13224', pubm...(truncated) 48,796 {} 2022-05-05 01:52:49
pypath.inputs.huri.lit_bm_interactions 2022-05-05 01:53:00 2022-05-05 01:54:46 106.00 list [LitBmInteraction(uniprot_a='P23511', uniprot_b='Q13952'), LitBmInteraction(uniprot_a='P23511', uniprot_b='P25208'), LitBmInteraction(uniprot_a='P43351', uniprot_b='P43351'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q92843'), LitBmInteraction(uniprot_a='Q92934', uniprot_b='Q07817'), LitBmInte...(truncated) 13,686 {} 2022-05-05 01:53:00
pypath.inputs.huri.rolland_hi_ii_14 2022-05-05 01:54:46 2022-05-05 01:54:49 2.57 list [['14', '6293', 'AAMP', 'VPS52', '1'], ['14', '8553', 'AAMP', 'BHLHE40', '1'], ['14', '64782', 'AAMP', 'AEN', '2'], ['15', '4188', 'AANAT', 'MDFI', '1'], ['15', '8553', 'AANAT', 'BHLHE40', '1'], ['28', '65983', 'ABO', 'GRAMD3', '2'], ['28', '84283', 'ABO', 'TMEM79', '1'], ['39', '39', 'ACAT2', 'ACAT...(truncated) 13,944 {} 2022-05-05 01:54:46
pypath.inputs.huri.vidal_hi_iii_old 
Not calling `pypath.inputs.huri.vidal_hi_iii_old`, not enough arguments.
 {} never
pypath.inputs.huri.yang2016_interactions 2022-05-05 01:54:49 2022-05-05 01:54:58 9.37 list [HuriInteraction(uniprot_a='P07196', uniprot_b='Q9BQQ3', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='O94989', uniprot_b='Q53EZ4', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q8NHQ1', uniprot_b='Q9H7H0', isoform_a=1, isoform_b=1, score=None), HuriInteractio...(truncated) 2,829 {} 2022-05-05 01:54:49
pypath.inputs.huri.yu2011_interactions 2022-05-05 01:54:58 2022-05-05 01:55:10 12.46 list [HuriInteraction(uniprot_a='Q5VUM1', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteraction(uniprot_a='P62166', uniprot_b='Q86UW9', isoform_a=1, isoform_b=1, score=None), HuriInteraction(uniprot_a='Q9NV12', uniprot_b='O43889', isoform_a=1, isoform_b=2, score=None), HuriInteractio...(truncated) 7,381 {} 2022-05-05 01:54:58
pypath.inputs.i3d.get_i3d 2022-05-05 01:55:10 2022-05-05 01:55:32 21.63 list [{'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P02647': {'pfam': None, 'chain': 'A', 'seq': [[68, 265]]}, 'uniprots': ['A0A024RAV5', 'P02647'], 'source': 'I3D', 'pdb': ['2mse'], 'references': []}, {'A0A024RAV5': {'pfam': None, 'chain': 'B', 'seq': [[1, 185]]}, 'P10398': {'pfam': N...(truncated) 15,984 {} 2022-05-05 01:55:10
pypath.inputs.icellnet._icellnet_get_components 
Not calling `pypath.inputs.icellnet._icellnet_get_components`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_entity 
Not calling `pypath.inputs.icellnet._icellnet_get_entity`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_references 
Not calling `pypath.inputs.icellnet._icellnet_get_references`, not enough arguments.
 {} never
pypath.inputs.icellnet._icellnet_get_resources 
Not calling `pypath.inputs.icellnet._icellnet_get_resources`, not enough arguments.
 {} never
pypath.inputs.icellnet.icellnet_annotations 2022-05-05 01:55:32 2022-05-05 01:55:32 0.37 dict {'P03971': {IcellnetAnnotation(role='ligand', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, Complex: COMPLEX:P36894_Q16671: {IcellnetAnnotation(role='receptor', family='Cytokine', subfamily=None, classification=('Cytokine', 'Tgf'))}, 'P36894': {IcellnetAnnotation(role='rec...(truncated) 688 {} 2022-05-05 01:55:32
pypath.inputs.icellnet.icellnet_complexes 2022-05-05 01:55:32 2022-05-05 01:55:33 0.12 dict {'COMPLEX:P36894_Q16671': Complex: COMPLEX:P36894_Q16671, 'COMPLEX:Q04771_Q16671': Complex: COMPLEX:Q04771_Q16671, 'COMPLEX:P27037_P37023': Complex: COMPLEX:P27037_P37023, 'COMPLEX:P37023_Q13705': Complex: COMPLEX:P37023_Q13705, 'COMPLEX:P37023_Q13873': Complex: COMPLEX:P37023_Q13873, 'COMPLEX:O0023...(truncated) 117 {} 2022-05-05 01:55:32
pypath.inputs.icellnet.icellnet_interactions 2022-05-05 01:55:33 2022-05-05 01:55:33 0.12 list [IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:P36894_Q16671, family='Cytokine', subfamily=None, classification=['Cytokine', 'Tgf'], resources=None, references=['32333774']), IcellnetRecord(ligand='P03971', receptor=Complex: COMPLEX:Q04771_Q16671, family='Cytokine', subfamily=None, class...(truncated) 743 {} 2022-05-05 01:55:33
pypath.inputs.ielm.get_ielm 
Not calling `pypath.inputs.ielm.get_ielm`, not enough arguments.
 {} never
pypath.inputs.ielm.get_ielm_huge 
Not calling `pypath.inputs.ielm.get_ielm_huge`, not enough arguments.
 {} never
pypath.inputs.innatedb.innatedb_interactions 2022-05-05 01:55:33 2022-05-05 01:55:41 8.30 list [InnatedbInteraction(source_uniprot='Q9Y6Y9', source_genesymbol='LY96', target_uniprot='O00206', target_genesymbol='TLR4', pmid='10359581'), InnatedbInteraction(source_uniprot='Q99836', source_genesymbol='MYD88', target_uniprot='O00206', target_genesymbol='TLR4', pmid='17228323'), InnatedbInteractio...(truncated) 19,036 {} 2022-05-05 01:55:33
pypath.inputs.instruct.get_instruct 2022-05-05 01:55:41 2022-05-05 01:55:51 9.75 list [{'Q05513': {'pfam': 'PF00069', 'chain': None, 'seq': [['252', '518']]}, 'uniprots': ['Q05513', 'Q05513'], 'source': 'Instruct', 'pdb': ['3pfq'], 'references': ['11078718', '15665819', '17203073', '18650932', '19920073', '21900206', '21911421', '9748166']}, {'P01106': {'pfam': 'PF02344', 'chain': No...(truncated) 11,470 {} 2022-05-05 01:55:41
pypath.inputs.instruct.get_instruct_offsets 2022-05-05 01:55:51 2022-05-05 01:55:52 1.02 dict {('10gs', 'P09211'): 0, ('11gs', 'P09211'): 0, ('12gs', 'P09211'): 0, ('13gs', 'P09211'): 0, ('14gs', 'P09211'): 0, ('16gs', 'P09211'): 0, ('17gs', 'P09211'): 0, ('18gs', 'P09211'): 0, ('19gs', 'P09211'): 0, ('1a00', 'P68871'): 0, ('1a00', 'P69905'): 0, ('1a01', 'P68871'): 0, ('1a01', 'P69905'): 0, ...(truncated) 11,620 {} 2022-05-05 01:55:51
pypath.inputs.intact._try_isoform 
Not calling `pypath.inputs.intact._try_isoform`, not enough arguments.
 {} never
pypath.inputs.intact.intact_interactions 2022-05-05 01:55:52 2022-05-05 01:59:58 246.29 list [IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', id_type_b='uniprot', pubmeds={'10542231'}, methods={'peptide array'}, interaction_types={'direct interaction'}, mi_score=0.77, isoform_a=None, isoform_b=None), IntactInteraction(id_a='P49418', id_b='Q05193', id_type_a='uniprot', i...(truncated) 70,962 {} 2022-05-05 01:55:52
pypath.inputs.integrins.get_integrins 2022-05-05 01:59:58 2022-05-05 01:59:59 0.94 set {'P11215', 'P17301', 'P20702', 'Q13683', 'P56199', 'P05556', 'P18564', 'P26012', 'Q13797', 'P26010', 'O75578', 'P16144', 'P08648', 'P05107', 'P18084', 'P23229', 'P53708', 'P26006', 'Q9UKX5', 'Q13349', 'P20701', 'P05106', 'P08514', 'P38570', 'P06756'} 25 {} 2022-05-05 01:59:58
pypath.inputs.intogen.intogen_annotations 2022-05-05 01:59:59 2022-05-05 02:00:00 0.66 dict {'P00519': {IntogenAnnotation(type='FUSION', role='Activating', curated=False, oncodrive_role_prob=nan)}, 'P42684': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncodrive_role_prob=0.811)}, 'Q13085': {IntogenAnnotation(type='MUTATION', role='Activating', curated=False, oncod...(truncated) 480 {} 2022-05-05 01:59:59
pypath.inputs.ipi._ipi_uniprot_pairs 
Not calling `pypath.inputs.ipi._ipi_uniprot_pairs`, not enough arguments.
 {} never
pypath.inputs.ipi.ipi_uniprot 2022-05-05 02:00:00 2022-05-05 02:00:00 0.27 dict {'IPI00807623': {'A0A183'}, 'IPI00396341': {'A0AUZ9'}, 'IPI00884975': {'A0AUZ9'}, 'IPI00884987': {'A0AUZ9'}, 'IPI00885003': {'A0AUZ9'}, 'IPI00855723': {'A0AV02'}, 'IPI00867607': {'A0AV02'}, 'IPI00793608': {'A0AV02'}, 'IPI00867726': {'A0AV02'}, 'IPI00867740': {'A0AV02'}, 'IPI00169342': {'A0AV96'}, 'I...(truncated) 51,106 {} 2022-05-05 02:00:00
pypath.inputs.iptmnet.iptmnet_interactions 2022-05-05 02:00:00 2022-05-05 02:02:14 134.25 list [IptmnetInteraction(enzyme='Q92793', substrate='O15265', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetylation', resaa='257', resnum='K', score=None, references=['19955365']), IptmnetInteraction(enzyme='Q09472', substrate='O15527', enzyme_isoform=None, substrate_isoform=1, ptm_type='acetyl...(truncated) 16,686 {} 2022-05-05 02:00:00
pypath.inputs.italk.italk_annotations 2022-05-05 02:02:14 2022-05-05 02:02:15 0.89 dict {'P01023': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'Q07954': {ItalkAnnotation(mainclass='receptor', subclass='other'), ItalkAnnotation(mainclass='receptor', subclass='growth factor')}, 'Q16613': {ItalkAnnotation(mainclass='ligand', subclass='other')}, 'P48039': {ItalkAnnotation(main...(truncated) 1,414 {} 2022-05-05 02:02:14
pypath.inputs.italk.italk_interactions 2022-05-05 02:02:15 2022-05-05 02:02:16 0.27 list [ItalkInteraction(ligand='P01023', receptor='Q07954', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P48039', classification='other'), ItalkInteraction(ligand='Q16613', receptor='P49286', classification='other'), ItalkInteraction(ligand='P12821', receptor='P50052', classificati...(truncated) 2,706 {} 2022-05-05 02:02:15
pypath.inputs.italk.italk_raw 2022-05-05 02:02:16 2022-05-05 02:02:16 0.01 DataFrame Pair.Name ... Classification 0 A2M_LRP1 ... other 1 AANAT_MTNR1A ... other 2 AANAT_MTNR1B ... other 3 ACE_AGTR2 ... other 4 ACE_BDKRB2 ... other ... ... ... ... 2644 CXCL8_KSHV ...(truncated) 2,649 {} 2022-05-05 02:02:16
pypath.inputs.kea.kea_enzyme_substrate 2022-05-05 02:02:16 2022-05-05 02:02:28 12.33 list [{'start': None, 'end': None, 'instance': None, 'substrate': 'P08581', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 1349, 'references': {'15475459'}, 'typ': 'phosphorylation'}, {'start': None, 'end': None, 'instance': None, 'substrate': 'P98161', 'kinase': 'P00519', 'resaa': 'Y', 'resnum': 432, 'refe...(truncated) 35,196 {} 2022-05-05 02:02:16
pypath.inputs.kea.kea_interactions 2022-05-05 02:02:28 2022-05-05 02:02:31 3.46 list [KeaRecord(enzyme='P00519', substrate='P08581', residue_type='Y', residue_offset=1349, pmid='15475459', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', residue_type='Y', residue_offset=432, pmid='12637538', resource='Kinexus'), KeaRecord(enzyme='P00519', substrate='P98161', resid...(truncated) 35,196 {} 2022-05-05 02:02:28
pypath.inputs.kegg.kegg_dbget 
Not calling `pypath.inputs.kegg.kegg_dbget`, not enough arguments.
 {} never
pypath.inputs.kegg.kegg_interactions 2022-05-05 02:02:32 2022-05-05 02:04:31 119.73 list [KeggInteraction(id_a='Q03113', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcriptional=False), KeggInteraction(id_a='O94763', id_b='Q15283', effect='activation', pathway='MAPK signaling pathway', mechanism='', is_direct=True, transcription...(truncated) 14,419 {} 2022-05-05 02:02:32
pypath.inputs.kegg.kegg_medicus 2022-05-05 02:04:31 2022-05-05 02:04:45 13.46 set {KeggMedicusRawInteraction(id_a='814', id_b='64764', name_a='CAMK4', name_b='CREB3L2', effect='stimulation', itype='post_translational', pw_type='variant', type_a='gene', type_b='gene', network_id='N00305'), KeggMedicusRawInteraction(id_a='C01190', id_b='2629v1', name_a='Glucosylceramide', name_b='G...(truncated) 12,601 {} 2022-05-05 02:04:31
pypath.inputs.kegg.kegg_medicus_complexes 2022-05-05 02:04:45 2022-05-05 02:04:46 1.59 dict {'COMPLEX:Q14185_Q96BJ8': Complex: COMPLEX:Q14185_Q96BJ8, 'COMPLEX:Q8TBF5_Q9H3S5': Complex: COMPLEX:Q8TBF5_Q9H3S5, 'COMPLEX:P24385_Q00534': Complex: COMPLEX:P24385_Q00534, 'COMPLEX:Q9NPP4_Q9ULZ3': Complex: COMPLEX:Q9NPP4_Q9ULZ3, 'COMPLEX:P10644_P17612': Complex: COMPLEX:P10644_P17612, 'COMPLEX:P0649...(truncated) 266 {} 2022-05-05 02:04:45
pypath.inputs.kegg.kegg_medicus_interactions 2022-05-05 02:04:46 2022-05-05 02:04:48 1.62 list [KeggMedicusInteraction(id_a='Q16566', id_b='Q70SY1', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translational', effect='stimulation'), KeggMedicusInteraction(id_a='Q15109', id_b='P01112', entity_type_a='protein', entity_type_b='protein', interaction_type='post_translat...(truncated) 9,383 {} 2022-05-05 02:04:46
pypath.inputs.kegg.kegg_pathway_annotations 2022-05-05 02:04:48 2022-05-05 02:04:55 6.94 dict {'P17535': {KeggPathway(pathway='MAPK signaling pathway')}, 'P62993': {KeggPathway(pathway='mTOR signaling pathway'), KeggPathway(pathway='Fc epsilon RI signaling pathway'), KeggPathway(pathway='Growth hormone synthesis, secretion and action'), KeggPathway(pathway='Phospholipase D signaling pathway'...(truncated) 2,575 {} 2022-05-05 02:04:48
pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons 2022-05-05 02:04:55 2022-05-05 02:04:55 0.53 dict {'A8K7J7': {KeggPathway(pathway='Galactose metabolism'), KeggPathway(pathway='Starch and sucrose metabolism'), KeggPathway(pathway='Amino sugar and nucleotide sugar metabolism'), KeggPathway(pathway='Butirosin and neomycin biosynthesis'), KeggPathway(pathway='Glycolysis / Gluconeogenesis'), KeggPath...(truncated) 813 {} 2022-05-05 02:04:55
pypath.inputs.kegg.kegg_pathways 2022-05-05 02:04:55 2022-05-05 02:05:02 7.04 tuple ({'MAPK signaling pathway': {'P17535', 'P62993', 'P0DMV9', 'P51452', 'P53041', 'O14733', 'P20936', 'Q96KG9', 'P21359', 'Q9Y4G8', 'P45983', 'Q03112', 'O60359', 'P36897', 'P30305', 'O15111', 'Q06413', 'P63162', 'Q9UPT6', 'P15336', 'P01137', 'Q13972', 'P80370', 'P35813', 'P01106', 'P46734', 'P35638', '...(truncated) 2 {} 2022-05-05 02:04:55
pypath.inputs.kinasedotcom.kinasedotcom_annotations 2022-05-05 02:05:02 2022-05-05 02:05:03 0.77 dict {'P31749': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'P31751': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'Q9Y243': {KinasedotcomAnnotation(group='AGC', family='Akt', subfamily=None)}, 'O14578': {KinasedotcomAnnotation(group='AGC', family='DMPK', ...(truncated) 503 {} 2022-05-05 02:05:02
pypath.inputs.kirouac2010.kirouac2010_interactions 2022-05-05 02:05:03 2022-05-05 02:05:05 1.75 list [Kiruac2010Interaction(ligand='ADIPOQ', receptor='ADIPOR'), Kiruac2010Interaction(ligand='AGRP', receptor='ATRN'), Kiruac2010Interaction(ligand='AREG', receptor='EGFR'), Kiruac2010Interaction(ligand='ANGPTL1', receptor='TEK'), Kiruac2010Interaction(ligand='ANGPTL2', receptor='TEK'), Kiruac2010Intera...(truncated) 267 {} 2022-05-05 02:05:03
pypath.inputs.laudanna.laudanna_directions 2022-05-05 02:05:05 2022-05-05 02:05:05 0.30 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/laudanna.py", line 57, in laudanna_directions
    LaudannaDirection(
TypeError: LaudannaDirection.__new__() missing 1 required positional argument: 'target_genesymbol'
{} 2022-01-08 00:09:37
pypath.inputs.laudanna.laudanna_effects 2022-05-05 02:05:05 2022-05-05 02:05:06 0.57 list [LaudannaEffect(source_genesymbol='EDNRA', target_genesymbol='NBN', effect='activation'), LaudannaEffect(source_genesymbol='TGFB1', target_genesymbol='TGFB1', effect='inhibition'), LaudannaEffect(source_genesymbol='EIF5B', target_genesymbol='RPL11', effect='activation'), LaudannaEffect(source_genesy...(truncated) 63,438 {} 2022-05-05 02:05:05
pypath.inputs.li2012.get_li2012 2022-05-05 02:05:06 2022-05-05 02:05:51 45.07 list [['BCR', 'BCR/177', 'ABL', 'PTPN SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['BCR', 'BCR/177', 'ABL', 'GRB2 SH2', 'CTK_Cytoplasm', 'ubiquitous', 'PPP'], ['CAV', 'CAV1/14', 'ABL', 'GRB7 SH2', 'CTK_Membrane', 'ubiquitous', 'PPP'], ['CBL', 'CBL/700', 'ABL', 'CRK SH2', 'CTK_Cytoplasm', 'ubiquitous', '...(truncated) 583 {} 2022-05-05 02:05:06
pypath.inputs.li2012.li2012_dmi 2022-05-05 02:05:51 2022-05-05 02:06:08 17.13 list [<ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue BCR-1:Y177:phosphorylation ['Li2012']>, <ABL1 => Residue CAV1-1:Y14:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Residue CBL-1:Y700:phosphorylation ['Li2012']>, <ABL1 => Resid...(truncated) 593 {} 2022-05-05 02:05:51
pypath.inputs.li2012.li2012_enzyme_substrate 2022-05-05 02:06:08 2022-05-05 02:06:08 0.03 list [{'substrate': 'BCR', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 177}, {'substrate': 'CAV1', 'kinase': 'ABL', 'instance': None, 'start': None, 'end': None, 'resaa': 'Y', 'resnum': 14}, {'substrate': 'CBL', 'kinase': 'ABL', 'instance': None, 'start': None, ...(truncated) 349 {} 2022-05-05 02:06:08
pypath.inputs.li2012.li2012_interactions 2022-05-05 02:06:08 2022-05-05 02:06:08 0.03 list [['ABL', 'BCR', 'CTK_Cytoplasm', 'phosphorylation'], ['BCR', 'PTPN', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['BCR', 'GRB2', 'CTK_Cytoplasm', 'phosphomotif_binding'], ['ABL', 'CAV1', 'CTK_Membrane', 'phosphorylation'], ['CAV1', 'GRB7', 'CTK_Membrane', 'phosphomotif_binding'], ['ABL', 'CBL', 'CTK_C...(truncated) 503 {} 2022-05-05 02:06:08
pypath.inputs.lincs.lincs_compounds 2022-05-05 02:06:08 2022-05-05 02:06:13 4.54 dict {'10001': LincsCompound(lincs='LSM-1001', chembl='CHEMBL14762', chebi='CHEBI:354.22', inchi='InChI=1S/C19H26N6O/c1-4-15(11-26)22-19-23-17(20-10-14-8-6-5-7-9-14)16-18(24-19)25(12-21-16)13(2)3/h5-9,12-13,15,26H,4,10-11H2,1-3H3,(H2,20,22,23,24)/t15-/m1/s1', inchi_key='BTIHMVBBUGXLCJ-OAHLLOKOSA-N', smil...(truncated) 1,320 {} 2022-05-05 02:06:08
pypath.inputs.lmpid.lmpid_dmi 2022-05-05 02:06:13 2022-05-05 02:06:14 1.60 list [{'motif_protein': 'P54253', 'domain_protein': 'P62258', 'instance': 'RRWSAP', 'motif_start': 772, 'motif_end': 777, 'domain_name': '14-3-3 domain', 'domain_name_type': 'name', 'refs': ['20037628', '12757707']}, {'motif_protein': 'P54253', 'domain_protein': 'P63104', 'instance': 'RRWSAP', 'motif_sta...(truncated) 1,170 {} 2022-05-05 02:06:13
pypath.inputs.lmpid.lmpid_interactions 2022-05-05 02:06:14 2022-05-05 02:06:15 0.58 list [['P62258', 'P54253', '20037628;12757707'], ['P63104', 'P54253', '20037628;12757707'], ['P63104', 'P04049', '8601312'], ['P27348', 'P04049', '8601312'], ['P31946', 'P04049', '8601312'], ['Q04917', 'P04049', '8601312'], ['P63104', 'Q99683', '10411906'], ['P63104', 'P98177', '14690436'], ['P62258', 'O...(truncated) 1,170 {} 2022-05-05 02:06:14
pypath.inputs.lmpid.load_lmpid 2022-05-05 02:06:15 2022-05-05 02:06:16 0.84 list [{'bait': 'P54253', 'prey': 'P62258', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P54253', 'prey': 'P63104', 'refs': ['20037628', '12757707'], 'pos': [772, 777], 'inst': 'RRWSAP', 'dom': '14-3-3 domain'}, {'bait': 'P04049', 'prey': 'P6310...(truncated) 1,170 {} 2022-05-05 02:06:15
pypath.inputs.lncdisease.lncdisease_interactions 2022-05-05 02:06:16 2022-05-05 02:06:16 0.19 list [LncdiseaseInteraction(source='7SK', target='ABO', source_type='RNA', target_type='RNA', mechanism='regulatory', organism='human', pmid='22522162'), LncdiseaseInteraction(source='7SK', target='Ars2', source_type='RNA', target_type='Protein', mechanism='regulatory', organism='human', pmid='22244333')...(truncated) 478 {} 2022-05-05 02:06:16
pypath.inputs.lncrnadb.lncrnadb_interactions 2022-05-05 02:06:16 2022-05-05 02:06:16 0.55 list [LncrnadbInteraction(lncrna='Maternal somatic nucleus RNAs', partner='Scan RNAs', type='transcript', organism='Paramecium tetraurelia', pmid='19103667'), LncrnadbInteraction(lncrna='G22', partner='PABP', type='protein', organism='Loris tardigradus', pmid='17175535'), LncrnadbInteraction(lncrna='G22'...(truncated) 773 {} 2022-05-05 02:06:16
pypath.inputs.locate.locate_localizations 2022-05-05 02:06:16 2022-05-05 02:08:13 116.75 dict {'P27824': {LocateAnnotation(source='HPRD', location='golgi apparatus', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='lysosomes', cls='typeI', pmid=None, score=None), LocateAnnotation(source='HPRD', location='nuclear envelope', cls='typeI', pmid=None, score=None), Lo...(truncated) 9,496 {} 2022-05-05 02:06:16
pypath.inputs.lrdb.lrdb_annotations 2022-05-05 02:08:13 2022-05-05 02:08:14 0.86 dict {'P01023': {LrdbAnnotation(role='ligand', cell_type=None, sources=('Fantom5', 'HPMR', 'HPRD'), references=('10652313',))}, 'Q07954': {LrdbAnnotation(role='receptor', cell_type=None, sources=('Fantom5', 'HPRD'), references=('127', '9716487')), LrdbAnnotation(role='receptor', cell_type=None, sources=(...(truncated) 1,536 {} 2022-05-05 02:08:13
pypath.inputs.lrdb.lrdb_interactions 2022-05-05 02:08:14 2022-05-05 02:08:14 0.03 list [LrdbRecord(ligand_genesymbol='A2M', receptor_genesymbol='LRP1', sources=['Fantom5', 'HPMR', 'HPRD'], references=['10652313'], ligand_cells=[], receptor_cells=[]), LrdbRecord(ligand_genesymbol='AANAT', receptor_genesymbol='MTNR1A', sources=['Fantom5', 'HPMR'], references=['12943195'], ligand_cells=[...(truncated) 3,251 {} 2022-05-05 02:08:14
pypath.inputs.macrophage._trim_gname 
Not calling `pypath.inputs.macrophage._trim_gname`, not enough arguments.
 {} never
pypath.inputs.macrophage.macrophage_interactions 2022-05-05 02:08:14 2022-05-05 02:08:14 0.28 list [MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16497931'), MacrophageInteraction(source_genesymbol='ATM', target_genesymbol='IKBKG', mechanism='Binding', directed='0', location='nucleus', pmid='16965765'), Macro...(truncated) 4,516 {} 2022-05-05 02:08:14
pypath.inputs.matrisome.__matrisome_annotations_2 2022-05-05 02:08:14 2022-05-05 02:08:33 18.68 set {'CHADL', 'MBL2', 'LTBP1', 'S100A11', 'PLXNA1', 'Ltbp4', 'VWA1', 'P4ha2', 'FNDC1', 'Srpx', 'CCL19', 'Serpind1', 'COL6A6', 'Srpx2', 'LGALS9', 'Ctgf', 'Serpinh1', 'Ltbp1', 'COL5A1', 'LMAN1', 'C1qtnf5', 'Wisp2', 'MMP12', 'PRELP', 'Lgals1', 'Lamc1', 'Hpx', 'Plxnb2', 'SVEP1', 'ADAM10', 'Tinagl1', 'Kng1',...(truncated) 744 {} 2022-05-05 02:08:14
pypath.inputs.matrisome.matrisome_annotations 2022-05-05 02:08:33 2022-05-05 02:08:36 3.10 dict {'Q7Z7G0': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'Q5JPC9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycoproteins', subsubclass=None)}, 'B4DSV9': {MatrisomeAnnotation(mainclass='Core matrisome', subclass='ECM Glycopro...(truncated) 1,064 {} 2022-05-05 02:08:33
pypath.inputs.matrixdb._matrixdb_protein_list 
Not calling `pypath.inputs.matrixdb._matrixdb_protein_list`, not enough arguments.
 {} never
pypath.inputs.matrixdb.matrixdb_annotations 2022-05-05 02:08:36 2022-05-05 02:08:45 8.39 dict {'O14579': {MatrixdbAnnotation(mainclass='membrane')}, 'P57737': {MatrixdbAnnotation(mainclass='membrane')}, 'O14681': {MatrixdbAnnotation(mainclass='membrane')}, 'P19525': {MatrixdbAnnotation(mainclass='membrane')}, 'P29033': {MatrixdbAnnotation(mainclass='membrane')}, 'O00231': {MatrixdbAnnotation...(truncated) 10,097 {} 2022-05-05 02:08:36
pypath.inputs.matrixdb.matrixdb_ecm_proteins 2022-05-05 02:08:45 2022-05-05 02:08:45 0.08 set {'P24593', 'P55083', 'O14905', 'P09382', 'Q6UY14', 'O00755', 'P98160', 'P21941', 'O75093', 'Q9P2N4', 'P10600', 'Q14314', 'Q96FE5', 'P21810', 'Q8IWL1', 'Q8IUL8', 'P51888', 'P52803', 'Q53GQ0', 'Q66K79', 'Q8WVF2', 'Q7RTW8', 'O00744', 'Q8WTR8', 'P22692', 'Q15582', 'Q8TE56', 'Q03167', 'Q9BQ16', 'Q9HCU0',...(truncated) 483 {} 2022-05-05 02:08:45
pypath.inputs.matrixdb.matrixdb_interactions 2022-05-05 02:08:45 2022-05-05 02:08:45 0.22 list [['P13497', 'Q15113', '20979576', 'protease assay'], ['O00206', 'P21810', '24480070', 'microscale thermophoresis'], ['P49747', 'O15232', '22521401', 'enzyme linked immunosorbent assay'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O60568', 'O60568', '20955792', 'molecular sieving'], ['O...(truncated) 425 {} 2022-05-05 02:08:45
pypath.inputs.matrixdb.matrixdb_membrane_proteins 2022-05-05 02:08:45 2022-05-05 02:08:49 4.49 set {'O14579', 'P57737', 'O14681', 'P19525', 'P29033', 'O00231', 'Q14289', 'Q9NRI5', 'Q9NS68', 'Q15077', 'P51589', 'Q8IXH8', 'P07384', 'O43306', 'Q9UF11', 'Q9UPI3', 'Q92629', 'Q08345', 'P43250', 'Q8IY50', 'Q9UHX3', 'P86790', 'P12830', 'A0A0A0MT89', 'Q96LB8', 'P22001', 'Q5TDP6', 'Q9H252', 'Q6ZNB7', 'Q6ZS...(truncated) 8,240 {} 2022-05-05 02:08:45
pypath.inputs.matrixdb.matrixdb_secreted_proteins 2022-05-05 02:08:49 2022-05-05 02:08:50 0.44 set {'Q7Z5A4', 'P22626', 'P62736', 'P30044', 'P24593', 'O00231', 'Q8N6C5', 'Q03169', 'P01601', 'Q04756', 'P07204', 'P60985', 'P07384', 'A0A0C4DH72', 'Q9P0W0', 'P21941', 'Q96NZ8', 'P08174', 'P0DMC3', 'Q08345', 'P01040', 'Q9P2N4', 'Q14314', 'O60383', 'P12830', 'Q9UHL4', 'Q9UKI3', 'Q96P15', 'A0A0A0MT89', '...(truncated) 2,923 {} 2022-05-05 02:08:49
pypath.inputs.mcam.mcam_cell_adhesion_molecules 2022-05-05 02:08:50 2022-05-05 02:08:51 1.02 set {'P13612', 'Q8TD84', 'Q13308', 'Q9Y4C0', 'Q6ZW63', 'P16150', 'Q04900', 'P16671', 'Q05084', 'Q99418', 'Q6MZF4', 'O95500', 'P08F94', 'P50895', 'O14525', 'O00548', 'Q08174', 'Q5ZPR3', 'Q9Y5B2', 'P34741', 'P42771', 'Q14773', 'P02751', 'P16284', 'P25942', 'Q8IUX7', 'Q13477', 'Q13835', 'Q7Z3B1', 'P11215',...(truncated) 103 {} 2022-05-05 02:08:50
pypath.inputs.membranome.membranome_annotations 2022-05-05 02:08:51 2022-05-05 02:10:33 101.98 list [('P08575', 'Plasma membrane', 'extracellular side'), ('P23468', 'Plasma membrane', 'extracellular side'), ('P10586', 'Plasma membrane', 'extracellular side'), ('P23470', 'Plasma membrane', 'extracellular side'), ('Q13332', 'Plasma membrane', 'extracellular side'), ('P23471', 'Plasma membrane', 'ext...(truncated) 2,385 {} 2022-05-05 02:08:51
pypath.inputs.mimp.get_kinase_class 2022-05-05 02:10:33 2022-05-05 02:10:33 0.14 dict {'groups': {'AGC': ['AKT1', 'AKT2', 'AKT3', 'DMPK1', 'DMPK2', 'MRCKb', 'MRCKa', 'MRCK', 'ROCK2', 'ROCK1', 'CRIK', 'BARK1', 'BARK2', 'GPRK4', 'GPRK5', 'GPRK6', 'RHOK', 'GPRK6', 'GPRK7', 'MAST3', 'MAST2', 'MAST1', 'MASTL', 'MAST4', 'NDR1', 'LATS1', 'LATS2', 'NDR2', 'PKACa', 'PKACb', 'PKACg', 'PRKX', '...(truncated) 4 {} 2022-05-05 02:10:33
pypath.inputs.mimp.mimp_enzyme_substrate 2022-05-05 02:10:33 2022-05-05 02:10:53 19.76 list [{'instance': 'VVGARRSSWRVISSI', 'kinase': 'PDKC', 'resaa': 'S', 'resnum': 60, 'npmid': 8, 'substrate_refseq': 'NM_003404', 'substrate': 'YWHAB', 'start': 53, 'end': 67, 'databases': ['HPRD', 'phosphoELM', 'PhosphoSite']}, {'instance': 'VVGARRSSWRVISSI', 'kinase': 'PRKCD', 'resaa': 'S', 'resnum': 60...(truncated) 17,030 {} 2022-05-05 02:10:33
pypath.inputs.mimp.mimp_interactions 2022-05-05 02:10:53 2022-05-05 02:10:53 0.35 list [['PDKC', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCD', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PRKCZ', 'YWHAB', ['HPRD', 'phosphoELM', 'PhosphoSite']], ['PDKC', 'YWHAH', ['phosphoELM', 'PhosphoSite']], ['ATM', 'EIF4EBP1', ['phosphoELM', 'PhosphoSite']], ['RORC', 'EIF4EBP1', ...(truncated) 17,030 {} 2022-05-05 02:10:53
pypath.inputs.mir2disease.mir2disease_interactions 2022-05-05 02:10:53 2022-05-05 02:10:53 0.31 list [Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='KRAS', year='2008', sentence="A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk."), Mir2diseaseInteraction(mirna='hsa-let-7a', target_genesymbol='HMGA2', year='2008'...(truncated) 805 {} 2022-05-05 02:10:53
pypath.inputs.mirbase.get_mirbase_aliases 2022-05-05 02:10:53 2022-05-05 02:10:54 0.08 tuple ({'MIMAT0000062': {'hsa-let-7a', 'hsa-let-7a-5p'}, 'MIMAT0000063': {'hsa-let-7b', 'hsa-let-7b-5p'}, 'MIMAT0000064': {'hsa-let-7c-5p', 'hsa-let-7c'}, 'MIMAT0000065': {'hsa-let-7d', 'hsa-let-7d-5p'}, 'MIMAT0000066': {'hsa-let-7e-5p', 'hsa-let-7e'}, 'MIMAT0000067': {'hsa-let-7f', 'hsa-let-7f-5p'}, 'MIM...(truncated) 2 {} 2022-05-05 02:10:53
pypath.inputs.mirbase.mirbase_ids 2022-05-05 02:10:54 2022-05-05 02:10:54 0.08 list [('MIMAT0000062', 'MI0000060'), ('MIMAT0000062', 'MI0000062'), ('MIMAT0000062', 'MI0000061'), ('MIMAT0000063', 'MI0000063'), ('MIMAT0000064', 'MI0000064'), ('MIMAT0000065', 'MI0000065'), ('MIMAT0000066', 'MI0000066'), ('MIMAT0000067', 'MI0000067'), ('MIMAT0000067', 'MI0000068'), ('MIMAT0000068', 'MI...(truncated) 3,027 {} 2022-05-05 02:10:54
pypath.inputs.mirbase.mirbase_mature 2022-05-05 02:10:54 2022-05-05 02:10:54 0.05 list [('MIMAT0000062', 'hsa-let-7a'), ('MIMAT0000062', 'hsa-let-7a-5p'), ('MIMAT0000063', 'hsa-let-7b'), ('MIMAT0000063', 'hsa-let-7b-5p'), ('MIMAT0000064', 'hsa-let-7c-5p'), ('MIMAT0000064', 'hsa-let-7c'), ('MIMAT0000065', 'hsa-let-7d'), ('MIMAT0000065', 'hsa-let-7d-5p'), ('MIMAT0000066', 'hsa-let-7e-5p...(truncated) 3,487 {} 2022-05-05 02:10:54
pypath.inputs.mirbase.mirbase_mature_all 2022-05-05 02:10:54 2022-05-05 02:10:54 0.08 list ['MIMAT0000062', 'MIMAT0000062', 'MIMAT0000062', 'MIMAT0000063', 'MIMAT0000064', 'MIMAT0000065', 'MIMAT0000066', 'MIMAT0000067', 'MIMAT0000067', 'MIMAT0000068', 'MIMAT0000069', 'MIMAT0000069', 'MIMAT0000070', 'MIMAT0000071', 'MIMAT0000072', 'MIMAT0000073', 'MIMAT0000074', 'MIMAT0000074', 'MIMAT00000...(truncated) 3,027 {} 2022-05-05 02:10:54
pypath.inputs.mirbase.mirbase_precursor 2022-05-05 02:10:54 2022-05-05 02:10:54 0.05 list [('MI0000060', 'hsa-let-7a-1L'), ('MI0000060', 'hsa-let-7a-1'), ('MI0000061', 'hsa-let-7a-2'), ('MI0000061', 'hsa-let-7a-2L'), ('MI0000062', 'hsa-let-7a-3L'), ('MI0000062', 'hsa-let-7a-3'), ('MI0000063', 'hsa-let-7b'), ('MI0000063', 'hsa-let-7bL'), ('MI0000064', 'hsa-let-7cL'), ('MI0000064', 'hsa-le...(truncated) 2,173 {} 2022-05-05 02:10:54
pypath.inputs.mirbase.mirbase_precursor_all 2022-05-05 02:10:54 2022-05-05 02:10:54 0.08 list ['MI0000060', 'MI0000062', 'MI0000061', 'MI0000063', 'MI0000064', 'MI0000065', 'MI0000066', 'MI0000067', 'MI0000068', 'MI0000069', 'MI0000115', 'MI0000070', 'MI0000071', 'MI0000071', 'MI0000072', 'MI0000073', 'MI0000075', 'MI0000074', 'MI0000076', 'MI0000077', 'MI0000078', 'MI0000079', 'MI0000485', ...(truncated) 3,027 {} 2022-05-05 02:10:54
pypath.inputs.mirbase.mirbase_precursor_to_mature 2022-05-05 02:10:54 2022-05-05 02:10:54 0.13 list [('hsa-let-7a-1L', 'MIMAT0000062'), ('hsa-let-7a-1L', 'MIMAT0004481'), ('hsa-let-7a-1', 'MIMAT0000062'), ('hsa-let-7a-1', 'MIMAT0004481'), ('hsa-let-7a-2', 'MIMAT0010195'), ('hsa-let-7a-2', 'MIMAT0000062'), ('hsa-let-7a-2', 'MIMAT0004481'), ('hsa-let-7a-2L', 'MIMAT0010195'), ('hsa-let-7a-2L', 'MIMAT...(truncated) 3,361 {} 2022-05-05 02:10:54
pypath.inputs.mirdeathdb.mirdeathdb_interactions 2022-05-05 02:10:54 2022-05-05 02:10:54 0.24 list [MirdeathdbInteraction(mirna='MIMAT0020823', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0000365', target_entrez='40009', organism=7227, pubmed='12679032', function='apoptosis_down'), MirdeathdbInteraction(mirna='MIMAT0020823...(truncated) 462 {} 2022-05-05 02:10:54
pypath.inputs.mirecords.mirecords_interactions 2022-05-05 02:10:54 2022-05-05 02:16:54 360.01 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/mirecords.py", line 53, in mirecords_interactions
    tbl = inputs_common.read_xls(c.fileobj.name)
AttributeError: 'Curl' object has no attribute 'fileobj'
{'broke': True} 2022-05-03 02:13:46
pypath.inputs.mirtarbase._mirtarbase_interactions 
Not calling `pypath.inputs.mirtarbase._mirtarbase_interactions`, not enough arguments.
 {} never
pypath.inputs.mirtarbase.mirtarbase_interactions 2022-05-05 02:16:54 2022-05-05 02:17:32 37.25 list [MirtarbaseInteraction(mirtarbase_id='MIRT003135', mirna_name='mmu-miR-122-5p', mirna_organism='Mus musculus', target_genesymbol='Cd320', target_entrez='54219', target_organism='Mus musculus', target_site='AGAGACTGGGGTCCTCAGACACTCCC', method='Luciferase reporter assay//qRT-PCR//Western blot', catego...(truncated) 21,560 {} 2022-05-05 02:16:54
pypath.inputs.mitab.mitab_field_list 
Not calling `pypath.inputs.mitab.mitab_field_list`, not enough arguments.
 {} never
pypath.inputs.mitab.mitab_field_uniprot 
Not calling `pypath.inputs.mitab.mitab_field_uniprot`, not enough arguments.
 {} never
pypath.inputs.mppi.mppi_interactions 2022-05-05 02:17:32 2022-05-05 02:17:32 0.29 list [['9867828', '9867828', 'P05109', 'SP', 'S100A8;CAGA;MRP8; calgranulin A (migration inhibitory factor-related protein 8)', '9606', 'P06702', 'SP', 'S100A9;CAGB;MRP14; calgranulin B (migration inhibitory factor-related protein 14)', '9606'], ['9867828', '9867828', 'P06702', 'SP', 'S100A9;CAGB;MRP14; ...(truncated) 777 {} 2022-05-05 02:17:32
pypath.inputs.msigdb.msigdb_annotations 2022-05-05 02:17:32 2022-05-05 02:17:51 19.25 dict {} 0 {} 2022-05-05 02:17:32
pypath.inputs.msigdb.msigdb_download 2022-05-05 02:17:51 2022-05-05 02:17:52 1.07 dict {} 0 {} 2022-05-05 02:17:51
pypath.inputs.msigdb.msigdb_download_collections 2022-05-05 02:17:52 2022-05-05 02:18:11 19.24 dict {('hallmark', 'h.all'): {}, ('positional', 'c1.all'): {}, ('chemical_and_genetic_perturbations', 'c2.cgp'): {}, ('biocarta_pathways', 'c2.cp.biocarta'): {}, ('kegg_pathways', 'c2.cp.kegg'): {}, ('pid_pathways', 'c2.cp.pid'): {}, ('reactome_pathways', 'c2.cp.reactome'): {}, ('wikipathways', 'c2.cp.wi...(truncated) 18 {} 2022-05-05 02:17:52
pypath.inputs.ncrdeathdb.ncrdeathdb_interactions 2022-05-05 02:18:11 2022-05-05 02:18:14 2.20 list [NcrdeathdbInteraction(ncrna='MIMAT0000062', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organism=6239), NcrdeathdbInteraction(ncrna='MIMAT0000063', target_gene='ain-1', ncrna_type='miRNA', pathway='autophagy', effect='down', pmid='23619095', organis...(truncated) 7,305 {} 2022-05-05 02:18:11
pypath.inputs.negatome.negatome_interactions 2022-05-05 02:18:14 2022-05-05 02:18:14 0.12 list [NegatomeInteraction(uniprot_a='Q6ZNK6', uniprot_b='Q9Y4K3', pmid='15047173', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='Q9NR31', uniprot_b='Q15797', pmid='17356069', method='coimmunoprecipitation'), NegatomeInteraction(uniprot_a='P11627', uniprot_b='P53986', pmid='20155396', me...(truncated) 2,171 {} 2022-05-05 02:18:14
pypath.inputs.netbiol._netbiol_interactions 
Not calling `pypath.inputs.netbiol._netbiol_interactions`, not enough arguments.
 {} never
pypath.inputs.netbiol.arn_interactions 2022-05-05 02:18:14 2022-05-05 02:18:14 0.15 list [ArnInteraction(source_uniprot='O15350', target_uniprot='O95352', is_direct='0', is_directed='1', effect='0', source_autophagy='0', target_autophagy='1', references='19001857'), ArnInteraction(source_uniprot='O15350', target_uniprot='Q9H1Y0', is_direct='0', is_directed='1', effect='0', source_autoph...(truncated) 95 {} 2022-05-05 02:18:14
pypath.inputs.netbiol.nrf2ome_interactions 2022-05-05 02:18:14 2022-05-05 02:18:14 0.14 list [Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='O15379', is_direct='1', is_directed='0', effect='0', references='18241676'), Nrf2omeInteraction(source_uniprot='O00221', target_uniprot='Q16236', is_direct='0', is_directed='1', effect='-1', references='18241676'), Nrf2omeInteraction(sourc...(truncated) 109 {} 2022-05-05 02:18:14
pypath.inputs.netpath.netpath_interactions 2022-05-05 02:18:14 2022-05-05 02:18:16 2.18 list [['IL4R', '3566', 'IL4R', '3566', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL4R', '3566', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleukin-4 (IL-4)'], ['IL2RG', '3561', 'IL2RG', '3561', '8266078', 'in vivo', 'physical interaction', 'Interleu...(truncated) 7,555 {} 2022-05-05 02:18:14
pypath.inputs.netpath.netpath_names 2022-05-05 02:18:16 2022-05-05 02:18:16 0.01 dict {'137': 'Advanced glycation end-products (AGE/RAGE)', '1': 'Alpha6 Beta4 Integrin', '2': 'Androgen receptor (AR)', '12': 'B cell receptor (BCR)', '76': 'Brain-derived neurotrophic factor (BDNF)', '129': 'Corticotropin-releasing hormone (CRH)', '4': 'Epidermal growth factor receptor (EGFR)', '25': 'F...(truncated) 35 {} 2022-05-05 02:18:16
pypath.inputs.netpath.netpath_pathway_annotations 2022-05-05 02:18:16 2022-05-05 02:18:33 16.70 dict {'Q15109': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'O95831': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P54819': {NetpathPathway(pathway='Advanced glycation end-products (AGE/RAGE)')}, 'P31749': {NetpathPathway(pathway='Interleukin-1 (IL-...(truncated) 1,869 {} 2022-05-05 02:18:16
pypath.inputs.ontology.listof_ontologies 2022-05-05 02:18:33 2022-05-05 02:18:35 1.63 dict {'maxo': 'Medical Action Ontology', 'aeo': 'Anatomical Entity Ontology', 'mco': 'Microbial Conditions Ontology', 'afo': 'Allotrope Merged Ontology Suite', 'mf': 'Mental Functioning Ontology', 'agro': 'Agronomy Ontology', 'mfmo': 'Mammalian Feeding Muscle Ontology', 'aism': 'Ontology for the Anatomy ...(truncated) 273 {} 2022-05-05 02:18:33
pypath.inputs.ontology.ontology 
Not calling `pypath.inputs.ontology.ontology`, not enough arguments.
 {} never
pypath.inputs.opm.opm_annotations 2022-05-05 02:18:35 2022-05-05 02:18:53 18.10 dict {'Q5T2W1': {OpmAnnotation(membrane='Eykaryo. plasma', family='FXYD regulators', transmembrane=True)}, 'P08842': {OpmAnnotation(membrane='Endoplasm. reticulum', family='Sulfatase', transmembrane=True)}, 'P59666': {OpmAnnotation(membrane='Secreted', family='Vertebrate defensin', transmembrane=False)},...(truncated) 405 {} 2022-05-05 02:18:35
pypath.inputs.oreganno.oreganno_interactions 2022-05-05 02:18:53 2022-05-05 03:18:53 3,600.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/oreganno.py", line 77, in oreganno_interactions
    for l in oreganno_raw():
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/oreganno.py", line 44, in oreganno_raw
    _ = next(data)
TypeError: 'NoneType' object is not an iterator
{} 2022-04-01 01:18:20
pypath.inputs.oreganno.oreganno_raw 2022-05-05 03:18:53 2022-05-05 04:18:53 3,600.07 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/oreganno.py", line 44, in oreganno_raw
    _ = next(data)
TypeError: 'NoneType' object is not an iterator
{} 2022-04-01 01:20:19
pypath.inputs.panglaodb.panglaodb_annotations 2022-05-05 04:18:53 2022-05-05 04:18:58 5.07 defaultdict defaultdict(<class 'set'>, {'P17538': {PanglaodbAnnotation(canonical_marker=True, cell_type='Acinar cells', organ='Pancreas', germ_layer='Endoderm', entity_type='protein', human=(True,), mouse=(True,), human_sensitivity=1.0, mouse_sensitivity=0.957143, human_specificity=0.000628931, mouse_specificit...(truncated) 4,807 {} 2022-05-05 04:18:53
pypath.inputs.panglaodb.panglaodb_raw 2022-05-05 04:18:58 2022-05-05 04:18:58 0.03 list [{'species': 'Mm Hs', 'official gene symbol': 'CTRB1', 'cell type': 'Acinar cells', 'nicknames': 'CTRB', 'ubiquitousness index': '0.017', 'product description': 'chymotrypsinogen B1', 'gene type': 'protein-coding gene', 'canonical marker': '1', 'germ layer': 'Endoderm', 'organ': 'Pancreas', 'sensiti...(truncated) 8,286 {} 2022-05-05 04:18:58
pypath.inputs.pathwaycommons._create_single_resource_method 
Not calling `pypath.inputs.pathwaycommons._create_single_resource_method`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons.pathwaycommons_interactions 2022-05-05 04:18:58 2022-05-05 04:19:27 28.77 list [PathwayCommonsInteraction(id_a='AAK1', interaction_type='controls-phosphorylation-of', id_b='AP2M1', resource='PhosphoSite'), PathwayCommonsInteraction(id_a='AAK1', interaction_type='controls-state-change-of', id_b='AP2M1', resource='PhosphoSite'), PathwayCommonsInteraction(id_a='AAK1', interaction...(truncated) 1,261,865 {} 2022-05-05 04:18:58
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pathwaycommons._pc_single_resource 
Not calling `pypath.inputs.pathwaycommons._pc_single_resource`, not enough arguments.
 {} never
pypath.inputs.pazar.pazar_interactions 2022-05-05 04:19:28 2022-05-05 04:19:28 0.49 list [PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='9571041'), PazarInteraction(tf='ENST00000265354', target='ENSG00000143632', pmid='12760745'), PazarInteraction(tf='ENST00000265354', target='ENSG...(truncated) 16,386 {} 2022-05-05 04:19:28
pypath.inputs.pdb.pdb_chains 2022-05-05 04:19:28 2022-05-05 04:19:35 6.77 tuple ({'P02185': [{'pdb': '101m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset': 1}, {'pdb': '102m', 'chain': 'A', 'chain_beg': 1, 'chain_end': 154, 'pdb_beg': 0, 'pdb_end': 153, 'uniprot_beg': 1, 'uniprot_end': 154, 'offset':...(truncated) 2 {} 2022-05-05 04:19:28
pypath.inputs.pdb.pdb_complexes 2022-05-05 04:19:37 2022-05-05 04:19:43 6.59 dict {'COMPLEX:P00720': Complex: COMPLEX:P00720, 'COMPLEX:P09211': Complex: COMPLEX:P09211, 'COMPLEX:P00817': Complex: COMPLEX:P00817, 'COMPLEX:P00963': Complex: COMPLEX:P00963, 'COMPLEX:P00669': Complex: COMPLEX:P00669, 'COMPLEX:P07378': Complex: COMPLEX:P07378, 'COMPLEX:P01837_P01869': Complex: COMPLEX...(truncated) 39,930 {'size': 55} 2022-05-05 04:19:37
pypath.inputs.pdb.pdb_uniprot 2022-05-05 04:19:43 2022-05-05 04:19:56 12.24 tuple ({'P02185': {('1dtm', 'X-ray', 2.13), ('2myb', 'X-ray', 1.9), ('2zsr', 'X-ray', 1.21), ('2spm', 'X-ray', 1.7), ('3k9z', 'X-ray', 1.72), ('4mxk', 'X-ray', 1.52), ('6f1a', 'X-ray', 2.4), ('1mgn', 'X-ray', 1.9), ('5hlx', 'X-ray', 1.5), ('1bvd', 'X-ray', 1.4), ('2g11', 'X-ray', 1.9), ('1mbi', 'X-ray', 2...(truncated) 2 {} 2022-05-05 04:19:43
pypath.inputs.pdzbase.pdzbase_interactions 2022-05-05 04:19:56 2022-05-05 04:19:57 1.12 list [PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P13569', isoform_ligand=1, genesymbol_pdz='NHERF-1', genesymbol_ligand='CFTR', pdz_domain=1, organism=9606, pubmed=9613608), PDZbaseInteraction(uniprot_pdz='O14745', isoform_pdz=1, uniprot_ligand='P40879', isoform_ligand=1, gen...(truncated) 339 {} 2022-05-05 04:19:56
pypath.inputs.pepcyber.pepcyber_details 
Not calling `pypath.inputs.pepcyber.pepcyber_details`, not enough arguments.
 {} never
pypath.inputs.pepcyber.pepcyber_interactions 2022-05-05 04:19:57 2022-05-05 04:32:48 771.27 list [PepcyberInteraction(ppdb_class='14-3-3', ppdb_genesymbol='LOC284100', substrate_genesymbol='Bad', binding_seq='SPFRGRSRpSAPPNLWAA', binding_pos=136, all_evidences='Inference', n_records=1, category='A', substrate_residue='S', ppdb_uniprot='A2RUB5', ppdb_refseq='XP_375443', substrate_uniprot='Q61337...(truncated) 5,590 {} 2022-05-05 04:19:57
pypath.inputs.pfam._pfam_uniprot 
Not calling `pypath.inputs.pfam._pfam_uniprot`, not enough arguments.
 {} never
pypath.inputs.pfam.pfam_names 2022-05-05 04:32:48 2022-05-05 04:32:49 0.73 tuple ({'PFAM_NAME': {'PFAM_ACCESSION'}, 'Globin': {'PF00042'}, 'AsnA': {'PF03590'}, 'Peptidase_S29': {'PF02907'}, 'RVP': {'PF00077'}, 'Pribosyltran': {'PF00156'}, 'C1-set': {'PF07654'}, 'PK': {'PF00224'}, 'PK_C': {'PF02887'}, 'Neur': {'PF00064'}, 'Aldedh': {'PF00171'}, 'Trypsin': {'PF00089'}, 'RnaseA': {...(truncated) 2 {} 2022-05-05 04:32:48
pypath.inputs.pfam.pfam_pdb 2022-05-05 04:32:49 2022-05-05 04:32:52 2.49 tuple ({'101m': {'PF00042': PfamDomain(chain='A', start=27, end=143)}, '12as': {'PF03590': PfamDomain(chain='B', start=9, end=245)}, '1a1q': {'PF02907': PfamDomain(chain='B', start=30, end=178)}, '1a30': {'PF00077': PfamDomain(chain='A', start=5, end=98)}, '1a3c': {'PF00156': PfamDomain(chain='A', start=4...(truncated) 2 {} 2022-05-05 04:32:49
pypath.inputs.pfam.pfam_regions 2022-05-05 04:32:52 2022-05-05 04:53:42 1,250.16 tuple ({}, {}) 2 {} 2022-05-05 04:32:52
pypath.inputs.pfam.pfam_uniprot 2022-05-05 04:53:42 2022-05-05 04:58:51 308.39 tuple ({'Q5VZE5': {'PF04112'}, 'Q8IWS0': set(), 'Q63HM2': {'PF05041'}, 'Q6P3X8': {'PF13843'}, 'P51160': {'PF00233', 'PF01590'}, 'O60664': {'PF03036'}, 'Q9NYY3': {'PF00069', 'PF00659'}, 'O00231': {'PF18503', 'PF01399', 'PF18055'}, 'P46939': {'PF00569', 'PF09069', 'PF00435', 'PF00307', 'PF00397', 'PF09068'}...(truncated) 2 {} 2022-05-05 04:53:42
pypath.inputs.phobius.phobius_annotations 2022-05-05 04:58:51 2022-05-05 04:58:51 0.86 dict {'P01920': {PhobiusAnnotation(tm_helices=1, signal_peptide=True, cytoplasmic=1, non_cytoplasmic=1)}, 'P18440': {PhobiusAnnotation(tm_helices=0, signal_peptide=False, cytoplasmic=0, non_cytoplasmic=1)}, 'P00740': {PhobiusAnnotation(tm_helices=0, signal_peptide=True, cytoplasmic=0, non_cytoplasmic=1)}...(truncated) 20,350 {} 2022-05-05 04:58:51
pypath.inputs.phosphatome.phosphatome_annotations 2022-05-05 04:58:51 2022-05-05 04:58:59 7.39 dict {'P09923': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True, has_catalytic_activity=True)}, 'P05186': {PhosphatomeAnnotation(fold='AP', family='AP', subfamily='AP', has_protein_substrates=True, has_non_protein_substrates=True...(truncated) 264 {} 2022-05-05 04:58:51
pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate 2022-05-05 04:58:59 2022-05-05 04:59:02 3.33 list [{'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 204, 'start': None, 'end': None, 'substrate': 'O14543', 'kinase': 'P06239', 'references': ['12783885'], 'experiment': 'LTP', 'organism': 'Homo sapiens'}, {'instance': None, 'isoform': 1, 'resaa': 'Y', 'resnum': 221, 'start': None, 'end': None...(truncated) 2,426 {} 2022-05-05 04:58:59
pypath.inputs.phosphoelm.phosphoelm_interactions 2022-05-05 04:59:02 2022-05-05 04:59:03 0.49 list [['P06239', 'O14543', '12783885', 'Homo sapiens'], ['P06239', 'O14543', '15173187', 'Homo sapiens'], ['P12931', 'O14746', '12808100', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'], ['P06241', 'O15117', '10570256', 'Homo sapiens'], ['P06241', 'O15117', '10409671', 'Homo sapiens'],...(truncated) 2,426 {} 2022-05-05 04:59:02
pypath.inputs.phosphoelm.phosphoelm_kinases 2022-05-05 04:59:03 2022-05-05 04:59:03 0.10 dict {'AAK1': 'Q2M2I8', 'Abl': 'P00519', 'Abl2': 'P42684', 'Abl_drome': 'P00522', 'Ack_drome': 'Q9VZI2', 'AFK': 'P80197', 'Akt1_drome': 'Q8INB9', 'ALK': 'Q9UM73', 'Atg1_drome': 'Q9VU14', 'ATM': 'Q13315', 'ATR': 'Q13535', 'Aurora A': 'O14965', 'Aurora B': 'Q96GD4', 'Axl': 'P30530', 'BCKDK': 'O14874', 'BLK...(truncated) 247 {} 2022-05-05 04:59:03
pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate 2022-05-05 04:59:03 2022-05-05 04:59:04 0.93 list [{'instance': 'SSYGISETTLEEIFL', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1242, 'score': 1.0162, 'substrate': 'ABCA1', 'start': 1235, 'end': 1249}, {'instance': 'SYGISETTLEEIFLK', 'kinase': 'CSNK2A1', 'resaa': 'T', 'resnum': 1243, 'score': 1.0455, 'substrate': 'ABCA1', 'start': 1236, 'end': 1250...(truncated) 4,417 {} 2022-05-05 04:59:03
pypath.inputs.phosphonetworks.phosphonetworks_interactions 2022-05-05 04:59:04 2022-05-05 04:59:04 0.02 list [['TNNI3K', 'HCLS1'], ['RIPK3', 'HLCS'], ['PAK1', 'EIF4H'], ['ZAP70', 'LCP2'], ['PIM2', 'SFRS16'], ['TTK', 'RBBP5'], ['STK40', 'PPP1R13L'], ['MAPK9', 'HNRPUL1'], ['MAPK11', 'MAPKAPK5'], ['PNCK', 'PPP2R5D'], ['MAPK8', 'PPARG'], ['LCK', 'VAV1'], ['MAPKAPK5', 'TBC1D22A'], ['MAP2K1', 'MAPK1'], ['STK17A'...(truncated) 1,821 {} 2022-05-05 04:59:04
pypath.inputs.phosphopoint.phosphopoint_directions 2022-05-05 04:59:04 2022-05-05 04:59:04 0.25 list [('AKT1', 'AKT1'), ('AKT1', 'AKT2'), ('AKT1', 'ESR2'), ('AKT1', 'PHLPP'), ('AKT1', 'APPL'), ('AKT1', 'TCL6'), ('AKT1', 'GRB10'), ('AKT1', 'HSP90AA1'), ('AKT1', 'HSP90AB1'), ('AKT1', 'APLP2'), ('AKT1', 'IKBKB'), ('AKT1', 'ILK'), ('AKT1', 'IMPDH2'), ('AKT1', 'IRS1'), ('AKT1', 'KRT10'), ('AKT1', 'MDM4'...(truncated) 9,269 {} 2022-05-05 04:59:04
pypath.inputs.phosphopoint.phosphopoint_interactions 2022-05-05 04:59:04 2022-05-05 04:59:04 0.01 list [PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT1', target_entrez='207', category='Category 2'), PhosphopointInteraction(source_genesymbol='AKT1', source_entrez='207', target_genesymbol='AKT2', target_entrez='208', category='Category 2'), PhosphopointInt...(truncated) 9,269 {} 2022-05-05 04:59:04
pypath.inputs.phosphosite._phosphosite_filter_organism 
Not calling `pypath.inputs.phosphosite._phosphosite_filter_organism`, not enough arguments.
 {} never
pypath.inputs.phosphosite.phosphosite_directions 2022-05-05 04:59:04 2022-05-05 04:59:04 0.01 list [['P28482', 'Q8N122'], ['Q9NYL2', 'Q9NYL2'], ['P12931', 'P00533'], ['O14757', 'P08631'], ['P45983', 'Q96I25'], ['Q02156', 'O14920'], ['P37173', 'P37173'], ['P31749', 'P49840'], ['Q13153', 'Q96P20'], ['P49840', 'P49840'], ['P45984', 'P46937'], ['P06493', 'Q9GZV5'], ['P11309', 'P52907'], ['O14757', 'Q...(truncated) 8,971 {} 2022-05-05 04:59:04
pypath.inputs.phosphosite.phosphosite_enzyme_substrate 2022-05-05 04:59:04 2022-05-05 04:59:05 0.36 list [{'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrate_org': 'human', 'residue': 'S52', 'motif': 'MILLsELsRRRIRsI', 'resaa': 'S', 'resnum': 52, 'start': 45, 'end': 59, 'instance': 'MILLSELSRRRIRSI'}, {'kinase': 'Q9BQI3', 'kinase_org': 'human', 'substrate': 'P05198', 'substrat...(truncated) 13,127 {} 2022-05-05 04:59:04
pypath.inputs.phosphosite.phosphosite_interactions 2022-05-05 04:59:05 2022-05-05 04:59:05 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_interactions_all 2022-05-05 04:59:05 2022-05-05 04:59:05 0.01 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 9,041 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_interactions_curated 2022-05-05 04:59:05 2022-05-05 04:59:05 0.00 list [['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;145302...(truncated) 4,309 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_interactions_new 2022-05-05 04:59:05 2022-05-05 04:59:05 0.00 tuple ([['Q05513', 'P27448', '', 'human', 'AB;MS', '21983960;15174125;15084291;23312004;24719451'], ['P28482', 'Q8N122', 'human', 'human', 'MA', '21071439'], ['Q9NYL2', 'Q9NYL2', 'human', 'human', 'AB;MA', '15342622'], ['P12931', 'P00533', 'human', 'human', 'AB;WB;MS;MA', '20628053;11960379;21278788;14530...(truncated) 2 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_interactions_noref 2022-05-05 04:59:05 2022-05-05 04:59:05 0.00 list [['P51451', 'P31995', 'human', 'human', 'MS', ''], ['O14757', 'O60343', 'human', 'human', 'MS', ''], ['Q96GD4', 'Q09666', 'human', 'human', 'MS', ''], ['O14757', 'Q96QD9', 'human', 'human', 'MS', ''], ['P06493', 'O14715', 'human', 'human', 'MS', ''], ['Q5S007', 'P04637', 'human', 'human', 'AB;WB;MA'...(truncated) 4,732 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_ptm_orthology 2022-05-05 04:59:05 2022-05-05 04:59:13 8.48 dict {('P31946', 1, 'T', 2, 9606, 'phosphorylation'): {10090: {('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation')}}, ('Q9CQV8', 1, 'T', 2, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'T', 2, 9606, 'phosphorylation')}}, ('Q9CQV8', 1, 'S', 6, 10090, 'phosphorylation'): {9606: {('P31946', 1, 'S', 6, 9606,...(truncated) 198,541 {} 2022-05-05 04:59:05
pypath.inputs.phosphosite.phosphosite_ptms 2022-05-05 04:59:14 2022-05-05 04:59:40 26.36 list [<PTM Residue YWHAB-1:T2:20q13.12>, <PTM Residue YWHAB-1:S6:20q13.12>, <PTM Residue YWHAB-1:Y21:20q13.12>, <PTM Residue YWHAB-1:T32:20q13.12>, <PTM Residue YWHAB-1:S39:20q13.12>, <PTM Residue YWHAB-1:S47:20q13.12>, <PTM Residue YWHAB-1:Y50:20q13.12>, <PTM Residue YWHAB-1:S59:20q13.12>, <PTM Residue ...(truncated) 239,701 {} 2022-05-05 04:59:14
pypath.inputs.phosphosite.phosphosite_regsites 2022-05-05 04:59:40 2022-05-05 04:59:42 1.83 dict {'P41181': [{'aa': 'K', 'res': '270', 'modt': 'ub', 'organism': 'human', 'pmids': {'21209006'}, 'induces': [], 'disrupts': [], 'isoform': 1, 'function': {'intracellular localization', 'protein degradation', 'phosphorylation'}, 'process': {''}, 'comments': 'stimulates phosphorylation of S261', 'posit...(truncated) 5,298 {} 2022-05-05 04:59:40
pypath.inputs.phosphosite.phosphosite_regsites_one_organism 2022-05-05 04:59:42 2022-05-05 04:59:43 0.73 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/phosphosite.py", line 516, in phosphosite_regsites_one_organism
    dict(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/phosphosite.py", line 521, in <lambda>
    homologene.homologene_uniprot_dict(
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 143, in homologene_uniprot_dict
    hge = homologene_dict(source, target, 'entrez')
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/homologene.py", line 105, in homologene_dict
    this_taxon = int(l[1].strip())
IndexError: list index out of range
{} 2022-05-02 05:23:12
pypath.inputs.phosphosite.regsites_tab 
Not calling `pypath.inputs.phosphosite.regsites_tab`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_bonds 
Not calling `pypath.inputs.pisa.pisa_bonds`, not enough arguments.
 {} never
pypath.inputs.pisa.pisa_interfaces 
Not calling `pypath.inputs.pisa.pisa_interfaces`, not enough arguments.
 {} never
pypath.inputs.pro.get_pro 2022-05-05 04:59:43 2022-05-05 05:05:43 360.02 Obo <OBO file `https://proconsortium.org/download/current/pro_reasoned.obo`> 0 {} 2022-05-05 04:59:43
pypath.inputs.pro.pro_mapping 2022-05-05 05:05:43 2022-05-05 05:05:43 0.39 list [('PR:000000005', 'P37173'), ('PR:000000005', 'P38438'), ('PR:000000005', 'Q62312'), ('PR:000000005', 'Q90999'), ('PR:000000007', 'A0A0G2KN81'), ('PR:000000009', 'Q16671'), ('PR:000000009', 'Q62893'), ('PR:000000009', 'Q8K592'), ('PR:000000010', 'O57472'), ('PR:000000010', 'Q24025'), ('PR:000000010'...(truncated) 319,353 {} 2022-05-05 05:05:43
pypath.inputs.progeny.progeny_annotations 2022-05-05 05:05:43 2022-05-05 05:06:00 16.96 dict {'P35250': {ProgenyAnnotation(pathway='JAK-STAT', weight=0.0012188579040493524, p_value=0.998388257483376), ProgenyAnnotation(pathway='VEGF', weight=-0.15684553639501156, p_value=0.8477560090795286), ProgenyAnnotation(pathway='Trail', weight=-0.8006773132589663, p_value=0.6240861307828072), ProgenyA...(truncated) 18,598 {} 2022-05-05 05:05:43
pypath.inputs.progeny.progeny_raw 2022-05-05 05:06:01 2022-05-05 05:06:03 1.77 DataFrame gene pathway weight p.value 1 RFC2 EGFR 1.470647 0.001655 2 ESRRA EGFR 0.178590 0.211838 3 HNRNPK EGFR 0.306699 0.084560 4 CBX6 EGFR -0.675507 0.017641 5 ASRGL1 EGFR -0.252328 0.295430 ... ... ... ...(truncated) 274,143 {} 2022-05-05 05:06:01
pypath.inputs.proteinatlas.get_proteinatlas 2022-05-05 05:06:03 2022-05-05 05:07:30 87.61 dict {'normal': {'adipose tissue:adipocytes': {'O43657': ('Not detected', 'Approved'), 'O60762': ('Medium', 'Approved'), 'Q8IZE3': ('Low', 'Approved'), 'Q9NSG2': ('Medium', 'Uncertain'), 'P09769': ('Not detected', 'Enhanced'), 'P08603': ('Not detected', 'Supported'), 'Q9BTY2': ('Not detected', 'Approved'...(truncated) 2 {} 2022-05-05 05:06:03
pypath.inputs.proteinatlas.proteinatlas_annotations 2022-05-05 05:07:32 2022-05-05 05:10:03 151.56 dict {'O43657': {ProtainatlasAnnotation(organ='thyroid cancer', tissue='thyroid cancer', level='Low', status=None, n_not_detected=2, n_low=2, n_medium=0, n_high=0, prognostic=False, favourable=True, score=0.2244, pathology=True), ProtainatlasAnnotation(organ='placenta', tissue='decidual cells', level='Lo...(truncated) 19,373 {} 2022-05-05 05:07:32
pypath.inputs.proteinatlas.proteinatlas_secretome_annotations 2022-05-05 05:10:05 2022-05-05 05:10:08 2.40 dict {'P10646': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'P20701': {ProteinatlasSecretomeAnnotation(mainclass='Intracellular or membrane-bound', secreted=False)}, 'Q9NPA2': {ProteinatlasSecretomeAnnotation(mainclass='Secreted to blood', secreted=True)}, 'Q03405': {...(truncated) 2,591 {} 2022-05-05 05:10:05
pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations 2022-05-05 05:10:08 2022-05-05 05:10:09 1.09 dict {'Q8IZE3': {ProteinatlasSubcellularAnnotation(location='Nuclear bodies', status='Uncertain'), ProteinatlasSubcellularAnnotation(location='Microtubules', status='Uncertain')}, 'P23511': {ProteinatlasSubcellularAnnotation(location='Nucleoplasm', status='Supported')}, 'Q9Y4W2': {ProteinatlasSubcellular...(truncated) 6,821 {} 2022-05-05 05:10:08
pypath.inputs.proteins.variants 2022-05-05 05:10:09 2022-05-05 05:37:49 1,659.80 list [VariationRecord(features=[{'type': 'VARIANT', 'begin': 86, 'end': 86, 'consequence': 'missense', 'wild_residue': 'K', 'mutated_residue': 'T', 'somatic': False, 'evidence': 'mixed'}], uniprot='A0A024QZ33'), VariationRecord(features=[{'type': 'VARIANT', 'begin': 90, 'end': 90, 'consequence': 'missens...(truncated) 45,167 {'fixed': True} 2022-05-05 05:10:09
pypath.inputs.protmapper.get_protmapper 2022-05-05 05:37:49 2022-05-05 05:37:55 6.38 tuple ([{'ID': '0', 'CTRL_NS': 'UP', 'CTRL_ID': 'Q02156', 'CTRL_GENE_NAME': 'PRKCE', 'CTRL_IS_KINASE': 'True', 'TARGET_UP_ID': 'P15336', 'TARGET_GENE_NAME': 'ATF2', 'TARGET_RES': 'T', 'TARGET_POS': '52', 'SOURCES': 'psp,reach,signor,sparser'}, {'ID': '1', 'CTRL_NS': 'FPLX', 'CTRL_ID': 'PKC', 'CTRL_GENE_NA...(truncated) 2 {} 2022-05-05 05:37:49
pypath.inputs.protmapper.protmapper_enzyme_substrate 2022-05-05 05:37:56 2022-05-05 05:37:56 0.62 list [{'kinase': 'Q02156', 'resaa': 'T', 'resnum': 52, 'references': {'22304920', '25728676', '24727247', '24357804', '25545367'}, 'substrate': 'P15336', 'databases': {'REACH', 'SIGNOR', 'Sparser', 'PhosphoSite'}}, {'kinase': 'Q02156', 'resaa': 'T', 'resnum': 280, 'references': {'24727247', '23708658'}, ...(truncated) 22,139 {} 2022-05-05 05:37:56
pypath.inputs.protmapper.protmapper_interactions 
Not calling `pypath.inputs.protmapper.protmapper_interactions`, not enough arguments.
 {} never
pypath.inputs.pubchem.pubchem_mapping 
Not calling `pypath.inputs.pubchem.pubchem_mapping`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pmid 
Not calling `pypath.inputs.pubmed.get_pmid`, not enough arguments.
 {} never
pypath.inputs.pubmed.get_pubmeds 
Not calling `pypath.inputs.pubmed.get_pubmeds`, not enough arguments.
 {} never
pypath.inputs.pubmed.only_pmids 
Not calling `pypath.inputs.pubmed.only_pmids`, not enough arguments.
 {} never
pypath.inputs.pubmed.open_pubmed 
Not calling `pypath.inputs.pubmed.open_pubmed`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_dict 
Not calling `pypath.inputs.pubmed.pmids_dict`, not enough arguments.
 {} never
pypath.inputs.pubmed.pmids_list 
Not calling `pypath.inputs.pubmed.pmids_list`, not enough arguments.
 {} never
pypath.inputs.ramilowski2015.ramilowski_interactions 2022-05-05 05:37:57 2022-05-05 05:37:57 0.42 list [Ramilowski2015Interaction(ligand='A2M', receptor='LRP1', references='', resources='HPMR;HPRD;STRING.binding;STRING.experiment;literature supported'), Ramilowski2015Interaction(ligand='AANAT', receptor='MTNR1A', references='', resources='HPMR;literature supported'), Ramilowski2015Interaction(ligand=...(truncated) 1,894 {} 2022-05-05 05:37:57
pypath.inputs.ramilowski2015.ramilowski_locations 2022-05-05 05:37:57 2022-05-05 05:38:24 26.83 dict {'P04217': {RamilowskiLocation(location='secreted', source='Consensus', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='UniProt', tmh=0, note=None, long_note=None), RamilowskiLocation(location='secreted', source='Consensus6', tmh=0, note=None, long_note=None), Rami...(truncated) 18,861 {} 2022-05-05 05:37:57
pypath.inputs.rdata._patch_rdata 2022-05-05 05:38:24 2022-05-05 05:38:24 0.00 NoneType None 0 {} 2022-05-05 05:38:24
pypath.inputs.rdata._rdata_data_frame_get_rownames 
Not calling `pypath.inputs.rdata._rdata_data_frame_get_rownames`, not enough arguments.
 {} never
pypath.inputs.rdata._rdata_list_get_names 
Not calling `pypath.inputs.rdata._rdata_list_get_names`, not enough arguments.
 {} never
pypath.inputs.reaction._bp_collect_resources 
Not calling `pypath.inputs.reaction._bp_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._process_controls 
Not calling `pypath.inputs.reaction._process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_resources 
Not calling `pypath.inputs.reaction._reactome_collect_resources`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_collect_species 
Not calling `pypath.inputs.reaction._reactome_collect_species`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_compartment 
Not calling `pypath.inputs.reaction._reactome_compartment`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_id 
Not calling `pypath.inputs.reaction._reactome_extract_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_extract_res 
Not calling `pypath.inputs.reaction._reactome_extract_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_id 
Not calling `pypath.inputs.reaction._reactome_id`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reaction 
Not calling `pypath.inputs.reaction._reactome_reaction`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_reactions 2022-05-05 05:38:24 2022-05-05 05:40:40 136.47 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/reaction.py", line 986, in _reactome_reactions
    for i in sp.find('bqbiol:haspart').find_all('rdf:li'):
AttributeError: 'NoneType' object has no attribute 'find_all'
{} 2022-01-08 00:48:01
pypath.inputs.reaction._reactome_reactions_et 2022-05-05 05:40:40 2022-05-05 05:40:42 2.03 tuple ({}, {}, {}) 3 {} 2022-05-05 05:40:40
pypath.inputs.reaction._reactome_res 
Not calling `pypath.inputs.reaction._reactome_res`, not enough arguments.
 {} never
pypath.inputs.reaction._reactome_species 
Not calling `pypath.inputs.reaction._reactome_species`, not enough arguments.
 {} never
pypath.inputs.reaction.acsn_biopax 2022-05-05 05:40:42 2022-05-05 05:40:52 9.82 list ['<?xml version="1.0" encoding="UTF-8"?>\n', '<rdf:RDF\n', ' xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n', ' xmlns:owl="http://www.w3.org/2002/07/owl#"\n', ' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n', ' xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"\n', ' xml:base="...(truncated) 190,854 {} 2022-05-05 05:40:42
pypath.inputs.reaction.acsn_interactions_2 
Not calling `pypath.inputs.reaction.acsn_interactions_2`, not enough arguments.
 {} never
pypath.inputs.reaction.get_acsn_effects 2022-05-05 05:40:52 2022-05-05 05:40:52 0.17 list [['FOXO3', 'PIK3CA', '*'], ['FOXO3', 'PIK3CB', '*'], ['FOXO3', 'PIK3CD', '*'], ['FOXO3', 'PIK3CG', '*'], ['AKT1', 'HOMER3', '*'], ['AKT2', 'HOMER3', '*'], ['AKT3', 'HOMER3', '*'], ['CDH2', 'HOMER3', '*'], ['CDK6', 'CDKN2B', '*'], ['ANAPC2', 'RSPO3', '*'], ['AXIN1', 'RSPO3', '*'], ['AXIN2', 'RSPO3', ...(truncated) 37,288 {} 2022-05-05 05:40:52
pypath.inputs.reaction.get_controls 
Not calling `pypath.inputs.reaction.get_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.get_interactions 
Not calling `pypath.inputs.reaction.get_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.get_reactions 2022-05-05 05:40:52 2022-05-05 05:44:38 225.23 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 785, in test_input
    for i, rec in enumerate(value_gen):
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/reaction.py", line 1187, in get_reactions
    rea.load_all()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/pyreact.py", line 1304, in load_all
    self.load_pid()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/pyreact.py", line 1159, in load_pid
    parser.process()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/pyreact.py", line 251, in process
    self.open_biopax()
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/utils/pyreact.py", line 295, in open_biopax
    self.opener = curl.FileOpener(self.biopax, **opener_args)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/share/curl.py", line 585, in __init__
    if type(file_param) in common.char_types else file_param.name
AttributeError: 'NoneType' object has no attribute 'name'
{} 2022-01-08 00:48:07
pypath.inputs.reaction.get_soup 
Not calling `pypath.inputs.reaction.get_soup`, not enough arguments.
 {} never
pypath.inputs.reaction.panther_biopax 2022-05-05 05:44:38 2022-05-05 05:44:38 0.17 dict {'BioPAX/Fructose_galactose_metabolism.owl': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/cache/762ca0e0a7ee6d1f14203c6255cf9b3a-BioPAX.tar.gz'>, 'BioPAX/B_cell_activation.owl': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_s...(truncated) 178 {'size': 178, 'type': {'previous': 'NoneType', 'current': 'dict'}} 2022-05-05 05:44:38
pypath.inputs.reaction.panther_interactions 
Not calling `pypath.inputs.reaction.panther_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.pid_biopax 2022-05-05 05:44:38 2022-05-05 05:44:39 1.68 NoneType None 0 {} 2022-05-05 05:44:38
pypath.inputs.reaction.pid_interactions 
Not calling `pypath.inputs.reaction.pid_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.process_complex 
Not calling `pypath.inputs.reaction.process_complex`, not enough arguments.
 {} never
pypath.inputs.reaction.process_controls 
Not calling `pypath.inputs.reaction.process_controls`, not enough arguments.
 {} never
pypath.inputs.reaction.process_reactions 
Not calling `pypath.inputs.reaction.process_reactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactions_biopax 
Not calling `pypath.inputs.reaction.reactions_biopax`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_biopax 2022-05-05 05:44:39 2022-05-05 05:50:40 360.03 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/reaction.py", line 92, in reactome_biopax
    fileobj = c.result[fname]
TypeError: 'NoneType' object is not subscriptable
{} 2022-04-27 06:05:03
pypath.inputs.reaction.reactome_bs 2022-05-05 05:50:40 2022-05-05 05:56:26 346.97 list [('R-HSA-1059683', <?xml version='1.0' encoding='utf-8' standalone='no'?> <sbml level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core"> <notes> <annotation> <p xmlns="http://www.w3.org/1999/xhtml">SBML generated from Reactome version 80 on 3/28/22, 2:56 AM using JSBML version 1....(truncated) 2,580 {} 2022-05-05 05:50:40
pypath.inputs.reaction.reactome_interactions 
Not calling `pypath.inputs.reaction.reactome_interactions`, not enough arguments.
 {} never
pypath.inputs.reaction.reactome_sbml 2022-05-05 05:56:42 2022-05-05 05:56:44 2.00 dict {'R-HSA-1059683.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/cache/9cfb9d56283cf7ad3077ba1f8a187542-homo_sapiens.3.1.sbml.tgz'>, 'R-HSA-109581.sbml': <ExFileObject name='/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-00480...(truncated) 2,580 {} 2022-05-05 05:56:42
pypath.inputs.scconnect.scconnect_annotations 2022-05-05 05:56:44 2022-05-05 05:56:45 0.98 dict {'P41273': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P20292': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='human')}, 'P01189': {ScconnectAnnotation(role='ligand', family=None, type=None, inferred_from='mouse'), ScconnectAnnota...(truncated) 3,285 {} 2022-05-05 05:56:44
pypath.inputs.scconnect.scconnect_complexes 2022-05-05 05:56:45 2022-05-05 05:56:45 0.19 set {Complex: COMPLEX:O75462_Q9UBD9, Complex: COMPLEX:P29459_P29460, Complex: COMPLEX:Q14213_Q8NEV9, Complex: COMPLEX:Q16552_Q96PD4, Complex: COMPLEX:P0DP23_P0DP24_P0DP25, Complex: COMPLEX:P01215_P01222, Complex: COMPLEX:P08476_P09529, Complex: COMPLEX:O15263, Complex: COMPLEX:P0DML2_P0DML3, Complex: CO...(truncated) 17 {} 2022-05-05 05:56:45
pypath.inputs.scconnect.scconnect_interactions 2022-05-05 05:56:45 2022-05-05 06:11:00 854.45 list [ScconnectInteraction(ligand_id='ML355', target_id='P18054', ligand_organism=None, target_organism=9606, ligand_type='small_molecule', target_type='protein', effect='Inhibition', references='24393039'), ScconnectInteraction(ligand_id='PKUMDL_MH_1001', target_id='P16050', ligand_organism=None, target...(truncated) 20,434 {} 2022-05-05 05:56:45
pypath.inputs.science.science_download 
Not calling `pypath.inputs.science.science_download`, not enough arguments.
 {} never
pypath.inputs.signalink.signalink_annotations 2022-05-05 06:11:00 2022-05-05 06:11:09 9.10 dict {'pathway': {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='Toll-like receptor'), Signal...(truncated) 2 {} 2022-05-05 06:11:00
pypath.inputs.signalink.signalink_function_annotations 2022-05-05 06:11:09 2022-05-05 06:11:09 0.59 dict {'P43403': {SignalinkFunction(function='Scaffold'), SignalinkFunction(function='Mediator')}, 'Q9NYJ8': {SignalinkFunction(function='Co-factor'), SignalinkFunction(function='Scaffold')}, 'O43318': {SignalinkFunction(function='Mediator')}, 'P15018': {SignalinkFunction(function='Ligand')}, 'P42702': {S...(truncated) 784 {} 2022-05-05 06:11:09
pypath.inputs.signalink.signalink_interactions 2022-05-05 06:11:09 2022-05-05 06:11:10 0.71 list [SignalinkInteraction(id_a='P20963', id_b='P43403', is_direct=True, is_directed=True, effect=0, pathways_a=['T-cell receptor'], pathways_b=['Receptor tyrosine kinase', 'T-cell receptor'], functions_a=[], functions_b=['Mediator', 'Scaffold'], references=['10358158', '10358164', '10562324', '10925299'...(truncated) 1,939 {} 2022-05-05 06:11:09
pypath.inputs.signalink.signalink_pathway_annotations 2022-05-05 06:11:10 2022-05-05 06:11:11 0.58 dict {'P20963': {SignalinkPathway(pathway='T-cell receptor')}, 'P43403': {SignalinkPathway(pathway='T-cell receptor'), SignalinkPathway(pathway='Receptor tyrosine kinase')}, 'Q9NYJ8': {SignalinkPathway(pathway='Receptor tyrosine kinase'), SignalinkPathway(pathway='Toll-like receptor'), SignalinkPathway(p...(truncated) 836 {} 2022-05-05 06:11:10
pypath.inputs.signor.signor_complexes 2022-05-05 06:11:11 2022-05-05 06:11:11 0.63 dict {'COMPLEX:P23511_P25208_Q13952': Complex NFY: COMPLEX:P23511_P25208_Q13952, 'COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4': Complex mTORC2: COMPLEX:P42345_P68104_P85299_Q6R327_Q8TB45_Q9BVC4, 'COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4': Complex mTORC1: COMPLEX:P42345_Q8N122_Q8TB45_Q96B36_Q9BVC4...(truncated) 3,217 {'size': 2} 2022-05-05 06:11:11
pypath.inputs.signor.signor_enzyme_substrate 2022-05-05 06:11:11 2022-05-05 06:11:34 22.88 list [{'typ': 'phosphorylation', 'resnum': 140, 'instance': 'AVERVTKSPGETSKP', 'substrate': 'Q9UNZ2', 'start': 133, 'end': 147, 'kinase': 'P06493', 'resaa': 'S', 'motif': 'AVERVTKSPGETSKP', 'enzyme_isoform': None, 'substrate_isoform': None, 'references': {'12810701'}}, {'typ': 'phosphorylation', 'resnum'...(truncated) 9,996 {} 2022-05-05 06:11:11
pypath.inputs.signor.signor_interactions 2022-05-05 06:11:34 2022-05-05 06:11:35 0.38 list [SignorInteraction(source='P23771', target='Q9UL17', source_isoform=None, target_isoform=None, source_type='protein', target_type='protein', effect='down-regulates', mechanism='', ncbi_tax_id='9606', pubmeds='16386358', direct=False, ptm_type='', ptm_residue='', ptm_motif=''), SignorInteraction(sour...(truncated) 36,836 {} 2022-05-05 06:11:34
pypath.inputs.signor.signor_pathway_annotations 2022-05-05 06:11:35 2022-05-05 06:15:04 209.07 dict {'P49841': {SignorPathway(pathway='Cell cycle: G1/S phase transition'), SignorPathway(pathway='Sonic Hedgehog'), SignorPathway(pathway='Insulin Signaling'), SignorPathway(pathway='PI3K/AKT Signaling'), SignorPathway(pathway='Cell cycle: G2/M phase transition'), SignorPathway(pathway='MTOR Signaling'...(truncated) 611 {} 2022-05-05 06:11:35
pypath.inputs.signor.signor_pathways 
Not calling `pypath.inputs.signor.signor_pathways`, not enough arguments.
 {} never
pypath.inputs.signor.signor_protein_families 2022-05-05 06:15:04 2022-05-05 06:15:04 0.00 dict {'SIGNOR-PF1': ['P28482', 'P27361'], 'SIGNOR-PF2': ['Q9HBW0', 'Q9UBY5', 'Q92633'], 'SIGNOR-PF3': ['O14610', 'O60262', 'Q9P2W3', 'P63215', 'P63211', 'P50150', 'P59768', 'P63218', 'P61952', 'Q9UK08', 'Q9UBI6', 'P50151'], 'SIGNOR-PF4': ['P28482', 'P27361'], 'SIGNOR-PF5': ['P01137', 'P10600', 'P61812'],...(truncated) 93 {} 2022-05-05 06:15:04
pypath.inputs.spike.spike_complexes 2022-05-05 06:15:04 2022-05-05 06:15:04 0.00 
Traceback (most recent call last):
  File "/home/omnipath/testing/pypath-inputs/./status-report.py", line 765, in test_input
    value = fun(*_args, **_kwargs)
  File "/home/omnipath/testing/pypath-inputs/pypath_inputs_status__20220505-004801/pypath/inputs/spike.py", line 192, in spike_complexes
    interactions = spike_interactions(high_confidence = high_confidence)
TypeError: spike_interactions() got an unexpected keyword argument 'high_confidence'
{} 2022-04-21 06:07:05
pypath.inputs.spike.spike_interactions 2022-05-05 06:15:04 2022-05-05 06:15:19 15.57 list [SpikeInteraction(entrez_a='554210', genesymbol_a='MIR429', entrez_b='55914', genesymbol_b='ERBB2IP', directed='1', pmids='20005803', integrity='2', effect='2', assay='', data_source='Published research', description='Luciferase activity assay', mechanism='N/A', regulation=True), SpikeInteraction(en...(truncated) 8,903 {} 2022-05-05 06:15:04
pypath.inputs.stitch.stitch_actions_interactions 2022-05-05 06:15:19 2022-05-05 06:17:13 113.54 list [StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='00010461', partner_b='ENSP00000170630', mechanism='expression', action=None, score=150), StitchActionsInteraction(partner_a='23627457', pa...(truncated) 21,773,491 {} 2022-05-05 06:15:19
pypath.inputs.stitch.stitch_links_interactions 2022-05-05 06:17:13 2022-05-05 06:19:02 109.48 list [StitchLinksInteraction(partner_a='91663464', partner_b='ENSP00000354652', experimental=989, prediction=0, database=0, textmining=0, combined_score=989, physical_combined_score=996), StitchLinksInteraction(partner_a='90668081', partner_b='ENSP00000317985', experimental=933, prediction=0, database=0,...(truncated) 150,645 {} 2022-05-05 06:17:13
pypath.inputs.string.string_effects 2022-05-05 06:19:02 2022-05-05 06:19:14 11.43 list [StringEffectsInteraction(source='ENSP00000216366', target='ENSP00000000233', effect='*'), StringEffectsInteraction(source='ENSP00000000233', target='ENSP00000216366', effect='*'), StringEffectsInteraction(source='ENSP00000222547', target='ENSP00000000233', effect='*'), StringEffectsInteraction(sour...(truncated) 2,250,122 {} 2022-05-05 06:19:02
pypath.inputs.string.string_links_interactions 2022-05-05 06:19:15 2022-05-05 06:20:01 46.06 list [StringLinksInteraction(protein_a='ENSP00000000233', protein_b='ENSP00000440005', neighborhood_score=0, fusion=0, cooccurence=50, coexpression=99, experimental=679, database=900, textmining=59, combined_score=969, physical_combined_score=740), StringLinksInteraction(protein_a='ENSP00000000233', prot...(truncated) 247,200 {} 2022-05-05 06:19:15
pypath.inputs.string.string_physical_interactions 2022-05-05 06:20:01 2022-05-05 06:20:03 1.63 list [StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000221957', experimental=483, database=600, textmining=821, combined_score=959), StringPhysicalInteraction(protein_a='ENSP00000000412', protein_b='ENSP00000438085', experimental=932, database=0, textmining=0, combined_score=932...(truncated) 83,896 {} 2022-05-05 06:20:01
pypath.inputs.surfaceome.surfaceome_annotations 2022-05-05 06:20:03 2022-05-05 06:20:06 2.87 dict {'A0AV02': (0.8363, 'Transporters', {'SLC', 'SLC12', 'APC'}), 'A0FGR9': (0.0465, 'Unclassified', {'Unclassified'}), 'A0PJK1': (0.8802, 'Transporters', {'SLC5', 'SLC', 'APC'}), 'A0PK11': (0.6108, 'Unclassified', {'Unclassified'}), 'A0ZSE6': (0.6327, 'Miscellaneous', {'Unknown_function', 'TMEM30'}), '...(truncated) 2,808 {} 2022-05-05 06:20:03
pypath.inputs.switches_elm.get_switches_elm 2022-05-05 06:20:06 2022-05-05 06:21:19 72.90 list [{'intramol': False, 'bindingsite_a': {'elm': ['LIG_SH2_STAT5']}, 'bs_a_start': [['1'], ['6'], ['1']], 'bs_a_end': [['1'], ['6'], ['4']], 'uniprot_a': ('O43561',), 'uniprot_b': ('P19174',), 'bindingsite_b': {'pfam': ['PF00017']}, 'bs_b_start': [['5'], ['5'], ['0']], 'bs_b_end': [['6'], ['3'], ['9']]...(truncated) 839 {} 2022-05-05 06:20:06
pypath.inputs.talklr.talklr_annotations 2022-05-05 06:21:19 2022-05-05 06:21:19 0.74 dict {'P01023': {TalklrAnnotation(role='ligand', pmid=None, putative=False)}, 'Q07954': {TalklrAnnotation(role='receptor', pmid=None, putative=False), TalklrAnnotation(role='receptor', pmid='11560994', putative=False), TalklrAnnotation(role='receptor', pmid='21054788', putative=False)}, 'Q16613': {Talklr...(truncated) 1,345 {} 2022-05-05 06:21:19
pypath.inputs.talklr.talklr_interactions 2022-05-05 06:21:19 2022-05-05 06:21:19 0.04 list [TalklrInteraction(ligand='A2M', receptor='LRP1', pmids=(), resources=('HPRD', 'STRING', 'HPMR'), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1A', pmids=(), resources=('HPMR',), putative=False), TalklrInteraction(ligand='AANAT', receptor='MTNR1B', pmids=(), resources=('HPMR',), ...(truncated) 2,422 {} 2022-05-05 06:21:19
pypath.inputs.talklr.talklr_raw 2022-05-05 06:21:19 2022-05-05 06:21:19 0.02 DataFrame Pair_Name Ligand_ApprovedSymbol ... Pair_Source Pair_Evidence 0 A2M_LRP1 A2M ... known literature supported 1 AANAT_MTNR1A AANAT ... known literature supported 2 AANAT_MTNR1B AANAT ... known l...(truncated) 2,422 {} 2022-05-05 06:21:19
pypath.inputs.tcdb.tcdb_annotations 2022-05-05 06:21:19 2022-05-05 06:21:26 6.54 dict {'P60201': {TcdbAnnotation(family='Myelin Proteolipid Protein (MPLP)', tcid='9.B.38.1.2')}, 'Q9NWF4': {TcdbAnnotation(family='Eukaryotic Riboflavin Transporter (E-RFT)', tcid='2.A.125.1.1')}, 'O00161': {TcdbAnnotation(family='Synaptosomal Vesicle Fusion Pore (SVF-Pore)', tcid='1.F.1.1.1')}, 'O00299'...(truncated) 2,055 {} 2022-05-05 06:21:19
pypath.inputs.tcdb.tcdb_classes 2022-05-05 06:21:26 2022-05-05 06:21:26 0.03 dict {'A0CIB0': ('1.A.17.1.13', '1.A.17'), 'A0CS82': ('9.B.82.1.5', '9.B.82'), 'A0CX44': ('1.A.3.2.4', '1.A.3'), 'A0D5K0': ('2.A.66.3.4', '2.A.66'), 'A0E9B5': ('9.B.38.2.1', '9.B.38'), 'A0ECD9': ('3.A.1.207.1', '3.A.1'), 'A0FKN5': ('2.A.53.2.9', '2.A.53'), 'A0JCJ5': ('1.B.1.1.7', '1.B.1'), 'A0JSP2': ('3....(truncated) 21,922 {} 2022-05-05 06:21:26
pypath.inputs.tcdb.tcdb_families 2022-05-05 06:21:26 2022-05-05 06:21:26 0.01 dict {'1.A.1': 'Voltage-gated Ion Channel (VIC)', '1.A.10': 'Glutamate-gated Ion Channel (GIC) of Neurotransmitter Receptors', '1.A.100': 'Rhabdoviridae Putative Viroporin, U5 (RV-U5)', '1.A.101': 'Peroxisomal Pore-forming Pex11 (Pex11)', '1.A.102': 'Influenza A viroporin PB1-F2 (PB1-F2)', '1.A.103': 'Si...(truncated) 1,671 {} 2022-05-05 06:21:26
pypath.inputs.tfcensus.tfcensus_annotations 2022-05-05 06:21:26 2022-05-05 06:21:27 0.64 dict {'P23511': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'Q96QS3': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P31270': {TfcensusAnnotation(tfcensus_class='a', tissue='uterus')}, 'P57073': {TfcensusAnnotation(tfcensus_class='a', tissue=None)}, 'P17010': {TfcensusAnnotation(tfcen...(truncated) 1,885 {} 2022-05-05 06:21:26
pypath.inputs.threedcomplex.threedcomplex_chains 2022-05-05 06:21:27 2022-05-05 06:21:56 29.04 dict {'code': {'ch_new': 'ch_old'}, '4b5m_1': {'L': 'L', 'A': 'A', 'V': 'V', 'U': 'U'}, '4b5m_2': {'W': 'W', 'M': 'M', 'B': 'B', 'X': 'X'}, '4b5m_3': {'N': 'N', 'Z': 'Z', 'C': 'C', 'Y': 'Y'}, '4abk_1': {'A': 'A'}, '1lsz_1': {'A': 'A'}, '3gll_1': {'C': 'A', 'A': 'A', 'B': 'A'}, '1hz6_4': {'C': 'C', 'A': '...(truncated) 174,325 {} 2022-05-05 06:21:27
pypath.inputs.threedcomplex.threedcomplex_contacts 2022-05-05 06:21:56 2022-05-05 06:24:22 146.57 set {ThreedcomplexContact(pdb='3wry_1', uniprot_1='A7M6E7', uniprot_2='P03587', chain_1='A', chain_2='C', n_residues=20.0, length_1=415, length_2=434, domain_s1=('',), domain_p1=('PF06792.6',), domain_s2=('',), domain_p2=('PF01443.13',), ident=False, homo=False), ThreedcomplexContact(pdb='2o53_1', unipr...(truncated) 260,284 {} 2022-05-05 06:21:56
pypath.inputs.threedcomplex.threedcomplex_ddi 2022-05-05 06:24:23 2022-05-05 06:27:12 168.92 list [<pypath.internals.intera.DomainDomain object at 0x7f2d60918640>, <pypath.internals.intera.DomainDomain object at 0x7f2d60918730>, <pypath.internals.intera.DomainDomain object at 0x7f2d609187f0>, <pypath.internals.intera.DomainDomain object at 0x7f2d609188b0>, <pypath.internals.intera.DomainDomain o...(truncated) 525,639 {} 2022-05-05 06:24:23
pypath.inputs.threedcomplex.threedcomplex_nresidues 2022-05-05 06:27:13 2022-05-05 06:27:21 7.92 dict {'3wry_1': {('A7M6E7', 'P03587'): 20.0}, '2o53_1': {('P45381', 'P45381'): 21.5}, '1j3i_1': {('P13922', 'P13922'): 20.0}, '4y77_1': {('P21242', 'P23639'): 3.0, ('P30657', 'P40302'): 11.5, ('P25451', 'P30656'): 21.5, ('P23638', 'P32379'): 1.5, ('P30656', 'P40303'): 7.0, ('P23638', 'P40302'): 1.5, ('P2...(truncated) 81,397 {} 2022-05-05 06:27:13
pypath.inputs.threedid.get_3did 2022-05-05 06:27:21 2022-05-05 07:00:49 2,008.38 tuple ([<pypath.internals.intera.DomainDomain object at 0x7f2d75ed8e20>, <pypath.internals.intera.DomainDomain object at 0x7f2d75ed8eb0>, <pypath.internals.intera.DomainDomain object at 0x7f2d75edbc40>, <pypath.internals.intera.DomainDomain object at 0x7f2d75ed9e40>, <pypath.internals.intera.DomainDomain ...(truncated) 2 {} 2022-05-05 06:27:21
pypath.inputs.threedid.get_3did_ddi 2022-05-05 07:00:50 2022-05-05 07:01:18 28.90 dict {('P30041', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}, ('PF00578', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0'], '3hy2': ['Q06830', 'Q9BYN0']}}}, ('Q13162', 'Q9BYN0'): {('PF10417', 'PF02195'): {'pdbs': {'2rii': ['Q06830', 'Q9BYN0...(truncated) 3,275,350 {} 2022-05-05 07:00:50
pypath.inputs.topdb.topdb_annotations 2022-05-05 07:02:21 2022-05-05 07:02:27 5.76 dict {'P05067': {TopdbAnnotation(membrane='Extracellular', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Extracellular', topology='Membrane', score=89, tmregions=1), TopdbAnnotation(membrane='Plasma membrane', topology='Inside', score=89, tmregions=1), TopdbAnnotation(membrane='Pla...(truncated) 1,246 {'size': 2} 2022-05-05 07:02:21
pypath.inputs.transmir.transmir_interactions 2022-05-05 07:02:27 2022-05-05 07:02:28 0.75 list [TransmirInteraction(tf_genesymbol='AGO2', mirna='hsa-mir-155', effect='Repression', pubmed='24263100'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-106b', effect='Activation', pubmed='24798859'), TransmirInteraction(tf_genesymbol='AHR', mirna='hsa-mir-132', effect='Activation', pubmed='...(truncated) 2,678 {} 2022-05-05 07:02:27
pypath.inputs.trip.take_a_trip 2022-05-05 07:02:28 2022-05-05 07:02:28 0.01 dict {'sc': {('P48995', 'Q12791'): [['TRPC1', '', 'BKca', 'Inference', '', '', '', '', '', 'Prediction', '19168436']], ('P48995', 'Q13873'): [['TRPC1', '', 'BMPR-2', 'Affinity purification-mass spectrometry', 'Not used as a bait', '', 'Mouse', 'Leg muscle', 'C2C12 lysates', '', '15188402']], ('P48995', '...(truncated) 5 {} 2022-05-05 07:02:28
pypath.inputs.trip.trip_find_uniprot 
Not calling `pypath.inputs.trip.trip_find_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_get_uniprot 
Not calling `pypath.inputs.trip.trip_get_uniprot`, not enough arguments.
 {} never
pypath.inputs.trip.trip_interactions 2022-05-05 07:02:28 2022-05-05 07:02:28 0.01 list [['P48995', 'Q12791', '19168436;25139746', 'Co-immunoprecipitation;Co-immunofluorescence staining', 'unknown'], ['P48995', 'Q08209', '23228564', 'Co-immunoprecipitation', 'unknown'], ['P48995', 'P62158', '11290752;12601176;11983166', 'Fluorescence probe labeling;Fusion protein-pull down assay;Calciu...(truncated) 359 {} 2022-05-05 07:02:28
pypath.inputs.trip.trip_process 2022-05-05 07:02:28 2022-05-05 07:02:28 0.01 dict {('P48995', 'Q12791'): {'refs': {'19168436', '25139746'}, 'methods': {'Co-immunoprecipitation', 'Co-immunofluorescence staining'}, 'tissues': {'HEK293', 'Rat vascular smooth muscle cell', 'Porcine coronary artery', 'Rat aortic vascular smooth muscle cell'}, 'effect': set(), 'regions': set()}, ('P489...(truncated) 359 {} 2022-05-05 07:02:28
pypath.inputs.trip.trip_process_table 
Not calling `pypath.inputs.trip.trip_process_table`, not enough arguments.
 {} never
pypath.inputs.unichem._unichem_mapping 
Not calling `pypath.inputs.unichem._unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.info 
Not calling `pypath.inputs.unichem.info`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_info 2022-05-05 07:02:28 2022-05-05 07:02:28 0.02 list [UnichemSource(number='1', label='chembl', name='ChEMBL', description='A database of bioactive drug-like small molecules and bioactivities abstracted from the scientific literature.', acquisition='Standard InChIs and Keys provided on ftp site for each release.'), UnichemSource(number='2', label='dru...(truncated) 40 {} 2022-05-05 07:02:28
pypath.inputs.unichem.unichem_mapping 
Not calling `pypath.inputs.unichem.unichem_mapping`, not enough arguments.
 {} never
pypath.inputs.unichem.unichem_sources 2022-05-05 07:02:28 2022-05-05 07:02:28 0.02 dict {'1': 'chembl', '2': 'drugbank', '3': 'pdb', '4': 'gtopdb', '5': 'pubchem_dotf', '6': 'kegg_ligand', '7': 'chebi', '8': 'nih_ncc', '9': 'zinc', '10': 'emolecules', '12': 'atlas', '14': 'fdasrs', '15': 'surechembl', '17': 'pharmgkb', '18': 'hmdb', '20': 'selleck', '21': 'pubchem_tpharma', '22': 'pubc...(truncated) 40 {} 2022-05-05 07:02:28
pypath.inputs.uniprot._all_uniprots 2022-05-05 07:02:28 2022-05-05 07:02:28 0.22 set {'D3DXF2', 'P57737', 'A0A140VJK9', 'E5RJ77', 'B0FY49', 'A0A669K9X0', 'M0QXR8', 'B3KV18', 'A6NJ38', 'A0A3G5C5M0', 'F8W020', 'A0A5C2FVS9', 'A8YQI5', 'A0A1S6Q3Z4', 'A0A0A0MT50', 'A0A0B6XK00', 'L8E7Z8', 'H7C401', 'B4DPG6', 'A0A2P9FIK5', 'A0A455JTT8', 'H0UI04', 'Q86TP3', 'A0A4P2SSM1', 'A0A5C2GI93', 'B2R5...(truncated) 204,185 {} 2022-05-05 07:02:28
pypath.inputs.uniprot._cleanup 2022-05-05 07:02:28 2022-05-05 07:02:28 0.00 NoneType None 0 {} 2022-05-05 07:02:28
pypath.inputs.uniprot._protein_datasheet 
Not calling `pypath.inputs.uniprot._protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot._remove 
Not calling `pypath.inputs.uniprot._remove`, not enough arguments.
 {} never
pypath.inputs.uniprot._swissprot_param 
Not calling `pypath.inputs.uniprot._swissprot_param`, not enough arguments.
 {} never
pypath.inputs.uniprot.all_swissprots 2022-05-05 07:02:28 2022-05-05 07:02:28 0.00 set {'P57737', 'P19525', 'O00231', 'Q14289', 'P60985', 'O43306', 'C9JSJ3', 'Q96NZ8', 'Q8IY50', 'P86790', 'P12830', 'Q8N4Y2', 'A0A0A0MT89', 'P22001', 'Q5TDP6', 'Q6ZNB7', 'Q9BXP2', 'Q8TBE7', 'Q8NGJ2', 'Q9Y6N7', 'Q9H246', 'Q9NY43', 'Q969H0', 'Q86UR1', 'Q99459', 'Q5XG87', 'A6NDZ8', 'Q7RTU0', 'Q66K80', 'O958...(truncated) 20,376 {} 2022-05-05 07:02:28
pypath.inputs.uniprot.all_trembls 2022-05-05 07:02:28 2022-05-05 07:02:45 17.29 set {'D3DXF2', 'A0A140VJK9', 'E5RJ77', 'B0FY49', 'A0A669K9X0', 'M0QXR8', 'B3KV18', 'A6NJ38', 'A0A3G5C5M0', 'F8W020', 'A0A5C2FVS9', 'A8YQI5', 'A0A1S6Q3Z4', 'A0A0A0MT50', 'A0A0B6XK00', 'L8E7Z8', 'H7C401', 'B4DPG6', 'A0A2P9FIK5', 'A0A455JTT8', 'H0UI04', 'Q86TP3', 'A0A4P2SSM1', 'A0A5C2GI93', 'B2R5I9', 'D6RD...(truncated) 183,809 {} 2022-05-05 07:02:28
pypath.inputs.uniprot.all_uniprots 2022-05-05 07:02:45 2022-05-05 07:02:45 0.00 set {'D3DXF2', 'P57737', 'A0A140VJK9', 'E5RJ77', 'B0FY49', 'A0A669K9X0', 'M0QXR8', 'B3KV18', 'A6NJ38', 'A0A3G5C5M0', 'F8W020', 'A0A5C2FVS9', 'A8YQI5', 'A0A1S6Q3Z4', 'A0A0A0MT50', 'A0A0B6XK00', 'L8E7Z8', 'H7C401', 'B4DPG6', 'A0A2P9FIK5', 'A0A455JTT8', 'H0UI04', 'Q86TP3', 'A0A4P2SSM1', 'A0A5C2GI93', 'B2R5...(truncated) 204,185 {} 2022-05-05 07:02:45
pypath.inputs.uniprot.deleted_uniprot_genesymbol 
Not calling `pypath.inputs.uniprot.deleted_uniprot_genesymbol`, not enough arguments.
 {} never
pypath.inputs.uniprot.get_db 2022-05-05 07:02:45 2022-05-05 07:02:45 0.00 set {'D3DXF2', 'P57737', 'A0A140VJK9', 'E5RJ77', 'B0FY49', 'A0A669K9X0', 'M0QXR8', 'B3KV18', 'A6NJ38', 'A0A3G5C5M0', 'F8W020', 'A0A5C2FVS9', 'A8YQI5', 'A0A1S6Q3Z4', 'A0A0A0MT50', 'A0A0B6XK00', 'L8E7Z8', 'H7C401', 'B4DPG6', 'A0A2P9FIK5', 'A0A455JTT8', 'H0UI04', 'Q86TP3', 'A0A4P2SSM1', 'A0A5C2GI93', 'B2R5...(truncated) 204,185 {} 2022-05-05 07:02:45
pypath.inputs.uniprot.get_uniprot_sec 2022-05-05 07:02:45 2022-05-05 07:02:46 0.64 list [['A0A023IN41', 'H0Y5F6'], ['A0A024QZ37', 'X5D2H9'], ['A0A024QZ45', 'Q9BX63'], ['A0A024QZA1', 'Q5TDG9'], ['A0A024QZG0', 'O75150'], ['A0A024QZR6', 'Q9UII6'], ['A0A024R056', 'A0A140VJJ8'], ['A0A024R072', 'Q96S94'], ['A0A024R077', 'Q96S94'], ['A0A024R079', 'G3V1E2'], ['A0A024R081', 'J3QRY6'], ['A0A024R...(truncated) 71,902 {} 2022-05-05 07:02:45
pypath.inputs.uniprot.init_db 2022-05-05 07:02:46 2022-05-05 07:02:46 0.24 NoneType None 0 {} 2022-05-05 07:02:46
pypath.inputs.uniprot.is_swissprot 
Not calling `pypath.inputs.uniprot.is_swissprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_trembl 
Not calling `pypath.inputs.uniprot.is_trembl`, not enough arguments.
 {} never
pypath.inputs.uniprot.is_uniprot 
Not calling `pypath.inputs.uniprot.is_uniprot`, not enough arguments.
 {} never
pypath.inputs.uniprot.protein_datasheet 
Not calling `pypath.inputs.uniprot.protein_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_data 
Not calling `pypath.inputs.uniprot.uniprot_data`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_families 2022-05-05 07:02:46 2022-05-05 07:02:52 5.76 dict {'P51451': {UniprotFamily(family='Protein kinase superfamily, Tyr protein kinase', subfamily='SRC')}, 'P09871': {UniprotFamily(family='Peptidase S1', subfamily=None)}, 'Q9ULX7': {UniprotFamily(family='Alpha-carbonic anhydrase', subfamily=None)}, 'Q01518': {UniprotFamily(family='CAP', subfamily=None)...(truncated) 14,355 {} 2022-05-05 07:02:46
pypath.inputs.uniprot.uniprot_history 
Not calling `pypath.inputs.uniprot.uniprot_history`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_history_recent_datasheet 
Not calling `pypath.inputs.uniprot.uniprot_history_recent_datasheet`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_keywords 2022-05-05 07:02:52 2022-05-05 07:02:59 6.82 dict {'P51451': {UniprotKeyword(keyword='Ubl conjugation'), UniprotKeyword(keyword='Transferase'), UniprotKeyword(keyword='SH2 domain'), UniprotKeyword(keyword='Kinase'), UniprotKeyword(keyword='Membrane'), UniprotKeyword(keyword='Cell membrane'), UniprotKeyword(keyword='Nucleotide-binding'), UniprotKeyw...(truncated) 20,376 {} 2022-05-05 07:02:52
pypath.inputs.uniprot.uniprot_locations 2022-05-05 07:02:59 2022-05-05 07:03:07 8.13 dict {'P51451': {UniprotLocation(location='Cell membrane', features=('Lipid-anchor',))}, 'A6H8Y1': {UniprotLocation(location='Nucleus', features=None)}, 'O60885': {UniprotLocation(location='Chromosome', features=None), UniprotLocation(location='Nucleus', features=None)}, 'P22223': {UniprotLocation(locati...(truncated) 16,856 {} 2022-05-05 07:02:59
pypath.inputs.uniprot.uniprot_ncbi_taxids_2 2022-05-05 07:03:07 2022-05-05 07:03:07 0.08 dict {648330: Taxon(ncbi_id=648330, latin='Aedes albopictus densovirus (isolate Boublik/1994)', english='AalDNV', latin_synonym=None), 10804: Taxon(ncbi_id=10804, latin='Adeno-associated virus 2', english='AAV-2', latin_synonym=None), 648242: Taxon(ncbi_id=648242, latin='Adeno-associated virus 2 (isolate...(truncated) 26,873 {} 2022-05-05 07:03:07
pypath.inputs.uniprot.uniprot_preprocess 
Not calling `pypath.inputs.uniprot.uniprot_preprocess`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_recent_version 
Not calling `pypath.inputs.uniprot.uniprot_recent_version`, not enough arguments.
 {} never
pypath.inputs.uniprot.uniprot_taxonomy 2022-05-05 07:03:07 2022-05-05 07:03:09 2.02 dict {'P00521': {'Abelson murine leukemia virus'}, 'P03333': {'Abelson murine leukemia virus'}, 'H8ZM73': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'H8ZM71': {'Balsam fir', 'Abies balsamea', 'Pinus balsamea'}, 'Q9MV51': {'Abies firma', 'Momi fir'}, 'O81086': {'Grand fir', 'Pinus grandis', 'Abie...(truncated) 552,780 {} 2022-05-05 07:03:07
pypath.inputs.uniprot.uniprot_tissues 2022-05-05 07:03:10 2022-05-05 07:03:18 7.99 dict {'P51451': {UniprotTissue(tissue='Lymphatic organs', level='undefined'), UniprotTissue(tissue='Leydig cells', level='undefined'), UniprotTissue(tissue='Striate ducts of salivary glands', level='undefined'), UniprotTissue(tissue='Pancreatic islets', level='undefined'), UniprotTissue(tissue='Hair foll...(truncated) 9,938 {} 2022-05-05 07:03:10
pypath.inputs.uniprot.uniprot_topology 2022-05-05 07:03:18 2022-05-05 07:03:43 24.92 dict {'P22223': {UniprotTopology(topology='Transmembrane', start=655, end=677), UniprotTopology(topology='Cytoplasmic', start=678, end=829), UniprotTopology(topology='Extracellular', start=108, end=654)}, 'Q9ULX7': {UniprotTopology(topology='Cytoplasmic', start=312, end=337), UniprotTopology(topology='Ex...(truncated) 5,217 {} 2022-05-05 07:03:18
pypath.inputs.uniprot.valid_uniprot 
Not calling `pypath.inputs.uniprot.valid_uniprot`, not enough arguments.
 {} never
pypath.inputs.wang._wang_process 
Not calling `pypath.inputs.wang._wang_process`, not enough arguments.
 {} never
pypath.inputs.wang.cui_interactions 2022-05-05 07:03:43 2022-05-05 07:03:46 2.93 list [WangInteraction(genesymbol_source='14-3-3', genesymbol_target='BAD', entrez_source='10971', entrez_target='572', effect='-', function_source='Anti-apoptotic', location_source='Intracellular', function_target='P-A', location_target='Intracellular'), WangInteraction(genesymbol_source='14-3-3', genesy...(truncated) 5,089 {} 2022-05-05 07:03:43
pypath.inputs.wang.hsn_interactions 2022-05-05 07:03:46 2022-05-05 07:03:50 3.97 list [HsnInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+'), HsnInteraction(genesymbol_source='TGFB1', genesymbol_target='TGFB1', entrez_source='7040', entrez_target='7040', effect='-'), HsnInteraction(genesymbol_source='EIF5B', genesym...(truncated) 62,937 {} 2022-05-05 07:03:46
pypath.inputs.wang.wang_annotations 2022-05-05 07:03:50 2022-05-05 07:03:54 4.16 dict {'NA': {WangAnnotation(function='Lipid', location='Cytosol'), WangAnnotation(function='Lipid', location='Membrane'), WangAnnotation(function='Phosphatase', location='Cytosol'), WangAnnotation(function='Ion', location='Cytosol'), WangAnnotation(function='Ribosome', location='Ribosomes'), WangAnnotati...(truncated) 1,544 {} 2022-05-05 07:03:50
pypath.inputs.wang.wang_interactions 2022-05-05 07:03:54 2022-05-05 07:03:54 0.14 list [WangInteraction(genesymbol_source='EDNRA', genesymbol_target='NBN', entrez_source='1909', entrez_target='4683', effect='+', function_source='Multiple Domain Transmembrane Proteins', location_source='Membrane', function_target='Transcription Factor', location_target='Intracellular'), WangInteraction...(truncated) 62,937 {} 2022-05-05 07:03:54
pypath.inputs.wojtowicz2020._id_translate 
Not calling `pypath.inputs.wojtowicz2020._id_translate`, not enough arguments.
 {} never
pypath.inputs.wojtowicz2020.wojtowicz2020_interactions 2022-05-05 07:03:54 2022-05-05 07:03:55 1.32 list [Wojtowicz2020Interaction(id_a='P01889', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q8IWK6', id_b='Q96LC7'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='P29460'), Wojtowicz2020Interaction(id_a='Q9BWV1', id_b='Q6PI73'), Wojtowicz2020Interaction(id_a='P17213', id_b='Q96A28'), Wojtowicz2020Intera...(truncated) 483 {} 2022-05-05 07:03:54
pypath.inputs.wojtowicz2020.wojtowicz2020_raw 2022-05-05 07:03:55 2022-05-05 07:03:55 0.13 list [Wojtowicz2020RawRecord(prey_uniprot_name='1B35', bait_uniprot_name='SIG10', prey_common_name='HLA-B', bait_common_name='Siglec-10', prey_gene_name='HLA-B', bait_gene_name='SIGLEC10', prey_bait_replicate1_od650=0.1343, prey_bait_replicate2_od650=0.1416, prey_bait_replicate3_od650=0.1386, prey_contro...(truncated) 495 {} 2022-05-05 07:03:55
pypath.inputs.zhong2015.zhong2015_annotations 2022-05-05 07:03:55 2022-05-05 07:03:56 0.21 dict {'P12830': {Zhong2015Annotation(type='iCAM')}, 'Q9Y6N8': {Zhong2015Annotation(type='iCAM')}, 'P55287': {Zhong2015Annotation(type='iCAM')}, 'P55290': {Zhong2015Annotation(type='iCAM')}, 'P55291': {Zhong2015Annotation(type='iCAM')}, 'O75309': {Zhong2015Annotation(type='iCAM')}, 'Q12864': {Zhong2015Ann...(truncated) 466 {} 2022-05-05 07:03:55

The OmniPath Team • Saez Lab • 2022-05-05