Commit ee894775 authored by Audrey BIHOUEE's avatar Audrey BIHOUEE
Browse files

Update for reference file missing

parent 132f1bf2
......@@ -48,6 +48,13 @@ if args.referencename:
references = json.load(f)
if(args.referencename in references):
d["reference"] = references[args.referencename]
else:
d["reference"] = dict()
d["reference"]["name"]="nameOfRef #match with scripts/corresIDorg.txt"
d["reference"]["description"]="Ref description"
d["reference"]["fasta"]="</path/to/fastfile.fasta>"
d["reference"]["gtf"]="</path/to/gtffile.gtf>"
d["reference"]["biomart"]="feb2014.archive.ensembl.org,ENSEMBL_MART_ENSEMBL,hsapiens_gene_ensembl #for example"
alphanum = re.compile('^[\w-]+$')
alphanumStartLetter = re.compile('^[a-zA-Z]+[\w-]+$')
......
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