| Previous changeset 0:9e31ea9fc7ea (2019-03-13) Next changeset 2:9ec42cb35abd (2019-06-19) |
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Commit message:
planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c |
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modified:
data_manager/resource_building.py data_manager/resource_building.xml |
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| diff -r 9e31ea9fc7ea -r f3507260b30f data_manager/resource_building.py --- a/data_manager/resource_building.py Wed Mar 13 06:30:42 2019 -0400 +++ b/data_manager/resource_building.py Tue Apr 16 07:46:59 2019 -0400 |
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| @@ -539,19 +539,18 @@ else : all_diseases="NA" - #get all tm domain + #get all tm domain nb_domains = 0 - if "domain" in data['entry']['annotationsByCategory'].keys(): - tm_domains = data['entry']['annotationsByCategory']["domain"] - for tm_domain in tm_domains : - if "properties" in tm_domain.keys() and tm_domain['properties']!=[]: - domains = tm_domains["properties"] - for domain in domains : - if domain["name"]=="region structure" and domain["value"]=="Helical" : - nb_domains+=1 + if "transmembrane-region" in data['entry']['annotationsByCategory'].keys(): + tm_domains = data['entry']['annotationsByCategory']["transmembrane-region"] + all_tm_domains = set() + for tm in tm_domains : + all_tm_domains.add(tm['cvTermName']) + nb_domains+=1 + print "nb domains ++" + print (nb_domains) - - 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,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence]) output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv" path = os.path.join(target_directory,output_file) |
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| diff -r 9e31ea9fc7ea -r f3507260b30f data_manager/resource_building.xml --- a/data_manager/resource_building.xml Wed Mar 13 06:30:42 2019 -0400 +++ b/data_manager/resource_building.xml Tue Apr 16 07:46:59 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.13" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.04.04" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> |