Mercurial > repos > dchristiany > data_manager_proteore
changeset 47:7b486b0fba4e draft
planemo upload commit cb633de1f04ef7b7133728909716b6c6594533d1-dirty
| author | dchristiany |
|---|---|
| date | Fri, 01 Feb 2019 10:30:00 -0500 |
| parents | 80fc0b28e227 |
| children | 4b6c6f9b4de0 |
| files | data_manager/resource_building.py data_manager/resource_building.xml |
| diffstat | 2 files changed, 10 insertions(+), 14 deletions(-) [+] |
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--- a/data_manager/resource_building.py Fri Feb 01 10:21:58 2019 -0500 +++ b/data_manager/resource_building.py Fri Feb 01 10:30:00 2019 -0500 @@ -279,16 +279,15 @@ # 4. Build protein interaction maps files ####################################################################################################### -def get_interactant_name(line): +def get_interactant_name(line,dico): - if line[0] in dico_geneid_to_gene_name : - print line[0] - interactant_A = dico_geneid_to_gene_name[line[0]] + if line[0] in dico : + interactant_A = dico[line[0]] else : interactant_A = "NA" - if line[1] in dico_geneid_to_gene_name : - interactant_B = dico_geneid_to_gene_name[line[1]] + if line[1] in dico : + interactant_B = dico[line[1]] else : interactant_B = "NA" @@ -426,12 +425,9 @@ dico_geneid_to_gene_name={} for line in humap_nodes : - if check_entrez_geneid(line[5]): - if line[5] not in dico_geneid_to_gene_name: - dico_geneid_to_gene_name[line[5]]=[line[4]] - else : - if line[4] not in dico_geneid_to_gene_name[line[5]] : - dico_geneid_to_gene_name[line[5]].append(line[4]) + 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] with requests.Session() as s: r = s.get('http://proteincomplexes.org/static/downloads/pairsWprob.txt')
--- a/data_manager/resource_building.xml Fri Feb 01 10:21:58 2019 -0500 +++ b/data_manager/resource_building.xml Fri Feb 01 10:30:00 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.02.01" tool_type="manage_data"> +<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.02.01.1" tool_type="manage_data"> <description> to create or update reference files for proteore tools </description> @@ -19,7 +19,7 @@ --id_mapping="$database.species" #else if $database.database == "PPI" --interactome="$database.base.interactome" - #if $database.base.interacome == "biogrid" + #if $database.base.interactome == "biogrid" --species="$database.base.species" #end if #end if