| Previous changeset 6:8f33a6e6e36c (2020-06-10) |
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Commit message:
"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7" |
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modified:
data_manager/resource_building.py data_manager/resource_building.xml |
| b |
| diff -r 8f33a6e6e36c -r b8565596bb25 data_manager/resource_building.py --- a/data_manager/resource_building.py Wed Jun 10 03:13:18 2020 -0400 +++ b/data_manager/resource_building.py Thu Aug 20 03:33:35 2020 -0400 |
| [ |
| @@ -554,10 +554,10 @@ name = "neXtProt release "+time.strftime("%d-%m-%Y") release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y") - output = open(path, 'w') + output = open('test.csv', 'w') writer = csv.writer(output,delimiter="\t") - nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]] + nextprot_file=[["NextprotID","ProteinName","SeqLength","MW","IsoPoint","TMDomains","SubcellLocations","Diseases","Function","PostTranslationalModifications","ProteinFamily","Pathway","ProteinExistence","Chr"]] writer.writerows(nextprot_file) for id in ids : @@ -565,8 +565,8 @@ try: resp = requests.get(url=query) except : - print ("wainting 1 hour before trying again") - time.sleep(3600) + print ("waiting 15 minutes before trying again") + time.sleep(900) resp = requests.get(url=query) data = resp.json() @@ -576,6 +576,38 @@ iso_elec_point = data['entry']["isoforms"][0]["isoelectricPointAsString"] chr_loc = data['entry']["chromosomalLocations"][0]["chromosome"] protein_existence = "PE"+str(data['entry']["overview"]['proteinExistence']['level']) + protein_name = data['entry']["overview"]['proteinNames'][0]['name'] + + #get families description + if 'families' in data['entry']["overview"] and len(data['entry']["overview"]['families']) > 0: + families = data['entry']["overview"]['families'] + families = [entry['description'] for entry in families] + protein_family = ";".join(families) + else: + protein_family = 'NA' + + #get Protein function + if 'function-info' in data['entry']['annotationsByCategory'].keys(): + function_info = data['entry']['annotationsByCategory']['function-info'] + function_info = [entry['description'] for entry in function_info if entry['qualityQualifier'] == 'GOLD'] + function = ';'.join(function_info) + else : + function = 'NA' + + #Get ptm-info + post_trans_mod = 'NA' + if 'ptm-info' in data['entry']['annotationsByCategory'].keys(): + ptm_info = data['entry']['annotationsByCategory']['ptm-info'] + infos = [entry['description'] for entry in ptm_info if entry['qualityQualifier'] == 'GOLD'] + post_trans_mod = ";".join(infos) + + #Get pathway(s) + if 'pathway' in data['entry']['annotationsByCategory'].keys(): + pathways = data['entry']['annotationsByCategory']['pathway'] + pathways = [entry['description'] for entry in pathways if entry['qualityQualifier'] == 'GOLD'] + pathway = ";".join(pathways) + else : + pathway = 'NA' #put all subcell loc in a set if "subcellular-location" in data['entry']["annotationsByCategory"].keys() : @@ -610,11 +642,12 @@ nb_domains+=1 #print "nb domains ++" #print (nb_domains) + nextprot_file[:] = [] - nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence]) + nextprot_file.append([id,protein_name,str(seq_length),mass_mol,iso_elec_point,str(nb_domains),all_subcell_locs,all_diseases,function,post_trans_mod,protein_family,pathway,protein_existence,chr_loc]) writer.writerows(nextprot_file) - id = str(10000000000 - int(time.strftime("%Y%m%d"))) + id = str(10000000000 - int(time.strftime("%Y%m%d"))) data_table_entry = dict(id=id, release=release_id, name = name, value = path) _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref") |
| b |
| diff -r 8f33a6e6e36c -r b8565596bb25 data_manager/resource_building.xml --- a/data_manager/resource_building.xml Wed Jun 10 03:13:18 2020 -0400 +++ b/data_manager/resource_building.xml Thu Aug 20 03:33:35 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.06.10" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.07.31" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> |