Mercurial > repos > proteore > proteore_data_manager
changeset 9:cdd29444e0af draft
planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty
| author | proteore |
|---|---|
| date | Tue, 12 Mar 2019 06:40:37 -0400 |
| parents | d5badf9de1b0 |
| children | e6b8f0e5fe16 |
| files | data_manager/resource_building.py data_manager/resource_building.xml |
| diffstat | 2 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/resource_building.py Tue Mar 12 05:43:54 2019 -0400 +++ b/data_manager/resource_building.py Tue Mar 12 06:40:37 2019 -0400 @@ -428,11 +428,14 @@ humap_nodes = csv.reader(r.splitlines(), delimiter=',') dico_geneid_to_gene_name={} + dico_protein_name={} for line in humap_nodes : if check_entrez_geneid(line[4]): if line[4] not in dico_geneid_to_gene_name: dico_geneid_to_gene_name[line[4]]=line[3] - + if line[4] not in dico_protein_name: + dico_protein_name[line[4]]=line[5] + with requests.Session() as s: r = s.get('http://proteincomplexes.org/static/downloads/pairsWprob.txt') r = r.content.decode('utf-8') @@ -477,6 +480,7 @@ dico['network']=dico_network dico['nodes']=dico_nodes dico['gene_name']=dico_geneid_to_gene_name + dico['protein_name']=dico_protein_name #writing output output_file = species+'_'+interactome+'_'+ time.strftime("%d-%m-%Y") + ".json"
--- a/data_manager/resource_building.xml Tue Mar 12 05:43:54 2019 -0400 +++ b/data_manager/resource_building.xml Tue Mar 12 06:40:37 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.12" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.12.1" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description>