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Now can take a VCF file as input 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3378 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-05-18 17:06:12 +00:00
parent e016491a3d
commit 886e9c1297
1 changed files with 11 additions and 2 deletions
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13
python/igvController.py
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@ -25,7 +25,7 @@ SLEEP_TIME = 1
def main():
global OPTIONS
usage = """usage: %prog [options] sites
Automatically captures IGV PNG screenshots at each site in the file sites (of the form chrX:start-stop or chrX:pos) by connecting to
Automatically captures IGV PNG screenshots at each site in the file sites (of the form chrX:start-stop or chrX:pos or a VCF file) by connecting to
an IGV session. See http://www.broadinstitute.org/igv/?q=PortCommands. Make sure you enable ports in the IGV preferences"""
parser = OptionParser(usage=usage)
parser.add_option("-w", "--wait", dest="wait",
@ -40,6 +40,9 @@ an IGV session. See http://www.broadinstitute.org/igv/?q=PortCommands. Make su
parser.add_option("-s", "--sort", dest="sort",
type='string', default="base",
help="The sort order for the bases, currently can be one of base, position, strand, quality, sample, and readGroup.")
parser.add_option("-p", "--prefix", dest="prefix",
type='string', default="",
help="A prefix to add before the contig name before sending the command to IGV. Useful for dealing with b36 -> hg18 issues")
(OPTIONS, args) = parser.parse_args()
if len(args) != 1:
@ -58,7 +61,13 @@ an IGV session. See http://www.broadinstitute.org/igv/?q=PortCommands. Make su
sendCommand("snapshotDirectory " + OPTIONS.dir + "\n")
c = 0
for line in open(sites):
site = line.split()[0]
parts = line.split()
if sites.find(".vcf") != -1 and parts[0][0] != "#":
site = OPTIONS.prefix + ':'.join(parts[0:2])
else:
site = parts[0]
print site
c+=1
sendCommand("goto %s\n" % site)