def __init__(self, dbname, dbuser, dbpass, wsuser, wspass, variant_url,
gbm_url):
# input is the CMS database name, user, and password and the
# GeneInsight web service user, password, and urls to
# both the Variant and genomeBuildMapping wsdls
# init database utility for geneinsight queries, connect to db
self.db = gi_util.CMS_DB(dbname, dbuser, dbpass)
# init GeneInsight class to query with web service for variant entries
self.gi_variant = Variant(wsuser, wspass, variant_url)
# init GeneInsight class to query with web service for transcript ids
self.gbm_ws = gi_util.GI_GenomeBuildMapping(wsuser=wsuser,
wspass=wspass,
wsurl=gbm_url)
# input is a chromosome, start position, end position
# test values
#chrom=13
#start=20763342
#end=20763342
wsurl = "https://geneinsight-lmm-ws.partners.org/services/GenomeBuildMapping?wsdl"
wsuser = "******"
wspass = "******"
try:
chrom = sys.argv[1]
start = sys.argv[2]
end = sys.argv[3]
except:
print "usage: gi_tid_by_region.py chromosome start_position end_position\ntest region: chrom=13, start=20763342, end=20763342"
exit(0)
gi_obj = gi_util.GI_GenomeBuildMapping(wsurl=wsurl,
wsuser=wsuser,
wspass=wspass)
tid = gi_obj.transcript_id(chrom, start, end)
if tid is None:
print "No transcript id found."
else:
print tid
exit(0)
parser.add_argument("--start", help="Start position (required)")
parser.add_argument("--end", help="End position (required)")
parser.add_argument(
"-w",
"--wsdl",
help="GeneInsight Variant WSDL (optional)(default GI 5.0 prod)",
default=default_gbm_wsdl)
parser.add_argument("-u",
"--user",
help="GeneInsight username (optional)(default lmm)",
default=default_user)
parser.add_argument("-p",
"--password",
help="GeneInsight password",
default=default_pass)
args = parser.parse_args()
if not args.chr or not args.start or not args.end:
raise Exception("coordinates required. missing chromosome, start, end")
#connect to geneinsight
gi_gbm = gi_util.GI_GenomeBuildMapping(wsurl=args.wsdl,
wsuser=args.user,
wspass=args.password)
info = gi_gbm.region_info(args.chr, args.start, args.end)
print str(info)
exit(0)