Mercurial > repos > estrain > ss2v102
diff SeqSero2_package.py @ 9:558823a8c53a tip
Uploaded
author | estrain |
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date | Thu, 03 Oct 2019 07:04:21 -0400 |
parents | 46b848d28b95 |
children |
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--- a/SeqSero2_package.py Thu Oct 03 06:29:10 2019 -0400 +++ b/SeqSero2_package.py Thu Oct 03 07:04:21 2019 -0400 @@ -1264,7 +1264,8 @@ #database="H_and_O_and_specific_genes.fasta" dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging - database=dirpath+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging + #database=ex_dir+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging + database="H_and_O_and_specific_genes.fasta" note="Note:" NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format if len(sys.argv)==1: @@ -1280,8 +1281,8 @@ subprocess.check_call(["mkdir",make_dir]) #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) - subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging - #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). + #subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging + subprocess.check_call("ln -f -s "+dirpath+"/seqsero2_db/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). ############################begin the real analysis if analysis_mode=="a": if data_type in ["1","2","3"]:#use allele mode