Mercurial > repos > zzhou > bamedit

comparison bamedit.py @ 53:19dfa6847218 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author zzhou
date Mon, 26 Nov 2012 14:01:06 -0500
parents 14b64c3d3250
children 948354e92a08
comparison
equal deleted inserted replaced
52:14b64c3d3250 53:19dfa6847218
9 import simplejson 9 import simplejson
10 10
11 CHUNK_SIZE = 1024 11 CHUNK_SIZE = 1024
12 12
13 def main(): 13 def main():
14 options = simplejson.load( open( sys.argv[1] ) ) 14 options = simplejson.load( open( sys.argv[1] ) )
15 15
16 16
17 shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH') 17 shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH')
18 print shscript 18 print shscript
19 testing = sys.argv[2] 19 testing = sys.argv[2]
20 print testing 20 print testing
21 if(options['action'] == "merge"): 21 if(options['action'] == "merge"):
22 cmdline = "samtools merge %s %s %s" % ( options['bamout'], options['input1'], options['input2'] ) 22 cmdline = "samtools merge %s %s %s" % ( options['bamout'], options['input1'], options['input2'] )
23 if('input3' in options): 23 if('input3' in options):
24 cmdline = "samtools merge %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] ) 24 cmdline = "samtools merge %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] )
25 elif (options['action'] == "split"): 25 elif (options['action'] == "split"):
26 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] ) 26 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )