Mercurial > repos > estrain > ss2v102

comparison SeqSero2_package.py @ 4:c4e40de653b9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Wed, 02 Oct 2019 20:47:51 -0400
parents 676a4588abe4
children ffc351049e31
comparison
equal deleted inserted replaced
3:a51d3bce2612 4:c4e40de653b9
1262 clean_mode=args.c 1262 clean_mode=args.c
1263 k_size=27 #will change for bug fixing 1263 k_size=27 #will change for bug fixing
1264 #database="H_and_O_and_specific_genes.fasta" 1264 #database="H_and_O_and_specific_genes.fasta"
1265 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) 1265 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
1266 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 1266 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
1267 database=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging 1267 database=dirpath+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging
1268 note="Note:" 1268 note="Note:"
1269 NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format 1269 NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format
1270 if len(sys.argv)==1: 1270 if len(sys.argv)==1:
1271 subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file 1271 subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file
1272 else: 1272 else: