Commit 132f1bf2 authored by Audrey BIHOUEE's avatar Audrey BIHOUEE
Browse files

Update for reference file missing

parent 2a078a20
{
"Ensembl_GRCh37":
{
"name":"Ensembl_GRCh37",
"description":"Homo sapiens Ensembl GRCh37",
"fasta":"CONFIG/genome/human_g1k_v37.chr22.fasta",
"gtf":"CONFIG/genome/chr22.gff",
"biomart":"feb2014.archive.ensembl.org,ENSEMBL_MART_ENSEMBL,hsapiens_gene_ensembl"
}
}
\ No newline at end of file
......@@ -43,11 +43,11 @@ d["read-length"] = args.readlength
d["align-cpu"] = "10"
# Get reference information
with open(os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))),"CONFIG","references.json")) as f:
references = json.load(f)
if(args.referencename in references):
d["reference"] = references[args.referencename]
if args.referencename:
with open(os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))),"CONFIG","references.json")) as f:
references = json.load(f)
if(args.referencename in references):
d["reference"] = references[args.referencename]
alphanum = re.compile('^[\w-]+$')
alphanumStartLetter = re.compile('^[a-zA-Z]+[\w-]+$')
......
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