Mercurial > repos > proteore > proteore_reactome
changeset 2:db63d069b5e6 draft
planemo upload commit a0b73386d86dc3d60ad33b944dad88fd5ff4d9ab-dirty
| author | proteore |
|---|---|
| date | Tue, 11 Dec 2018 07:46:12 -0500 |
| parents | 8200968789c1 |
| children | 988a6f43acdb |
| files | reactome_analysis.py reactome_analysis.xml |
| diffstat | 2 files changed, 7 insertions(+), 8 deletions(-) [+] |
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--- a/reactome_analysis.py Fri Dec 07 10:43:57 2018 -0500 +++ b/reactome_analysis.py Tue Dec 11 07:46:12 2018 -0500 @@ -43,8 +43,6 @@ trash = [] if identifiers[1] == "list": ids = "\n".join(id_valid(identifiers[0].split())[0]) - #print(ids) - #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids) json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read() if len(id_valid(identifiers[0].split())[1]) > 0: trash = id_valid(identifiers[0].split())[1] @@ -57,12 +55,13 @@ else: idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq] ids = "\n".join(id_valid(idens)[0]) - #print(ids) - #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids) - json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read() + json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> /dev/null" % ids).read() if len(id_valid(idens)[1]) > 0: trash = id_valid(idens)[1] - print(json_string) + #print(json_string) + j = json.loads(json_string) + print ("Identifiers not found: " + str(j["identifiersNotFound"])) + print ("Pathways found: " + str(j["pathwaysFound"])) return json_string, trash def write_output(filename, json_string, species, trash_file, trash): @@ -83,7 +82,7 @@ output.close() if trash: - print(trash) + #print(trash) trash_out = open(trash_file, "w") trash_out.write("\n".join(trash)) trash_out.close()
--- a/reactome_analysis.xml Fri Dec 07 10:43:57 2018 -0500 +++ b/reactome_analysis.xml Tue Dec 11 07:46:12 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="reactome_analysis" name="Reactome" version="2018.12.07"> +<tool id="reactome_analysis" name="Reactome" version="2018.12.11"> <description>display your protein list on the Reactome pathway browser</description> <requirements> </requirements>