Mercurial > repos > estrain > data_manager_fastani
changeset 14:0e06e944120b draft
Uploaded
| author | estrain |
|---|---|
| date | Sun, 29 May 2022 22:25:50 +0000 |
| parents | 8897c156df99 |
| children | ca9eecfb4b44 |
| files | data_manager_fastani/data_manager/data_manager_fastani.py |
| diffstat | 1 files changed, 6 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager_fastani/data_manager/data_manager_fastani.py Sun May 29 21:44:36 2022 +0000 +++ b/data_manager_fastani/data_manager/data_manager_fastani.py Sun May 29 22:25:50 2022 +0000 @@ -24,15 +24,12 @@ r = requests.get(url) f.write(r.content) - tarcmd="tar xvzf D1.tar.gz; rm -Rf D1.tar.gz" + tarcmd="tar xvzf D1.tar.gz; mv D1/* .; rm -Rf D1 D1.tar.gz" os.system(tarcmd) - cmd="mv D1 " + argsname - os.system(cmd) - os.chdir(cwd) - return output_directory + "/" + argsname + return def download_VL(output_directory): @@ -55,7 +52,7 @@ ecmd = "efetch -db nuccore -id " + acc + " -format fasta > " + accdict[acc] + ".fna" os.chdir(cwd) - return output_directory + return def print_json (version,argspath,argsname,argsout): @@ -93,11 +90,11 @@ #Fetch the files and build blast databases if(args.type[0]=="D1"): - output_directory=download_D1(output_directory,args.name[0]) + download_D1(output_directory) version="FastANI D1" elif(args.type[0]=="VL"): - output_directory=download_D1(output_directory,args.name[0]) - output_directory=download_VL(output_directory) + download_D1(output_directory) + download_VL(output_directory) version="FastANI D1 + VetLIRN" print_json(version,output_directory,args.name[0],args.out[0])