Mercurial > repos > zzhou > bamedit
changeset 51:0e5d77e4d9bf draft
Uploaded
| author | zzhou |
|---|---|
| date | Mon, 26 Nov 2012 13:56:54 -0500 |
| parents | d913c7afea82 |
| children | 14b64c3d3250 |
| files | bamedit.py |
| diffstat | 1 files changed, 7 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/bamedit.py Mon Nov 26 13:56:48 2012 -0500 +++ b/bamedit.py Mon Nov 26 13:56:54 2012 -0500 @@ -11,23 +11,20 @@ CHUNK_SIZE = 1024 def main(): - options = simplejson.load( open( sys.argv[1] ) ) + options = simplejson.load( open( sys.argv[1] ) ) - asdf = options['asdf'] - print "asdf %s" % asdf - shscript = sys.argv[2] - print shscript - - test1 = sys.argv[3] - - plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH') - if(options['action'] == "merge"): + shscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH') + plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH') + print plscript + if(options['action'] == "merge"): cmdline = "samtools merge %s %s %s" % ( options['bamout'], options['input1'], options['input2'] ) if('input3' in options): cmdline = "samtools merge %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] ) elif (options['action'] == "split"): #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] ) + asdf = options['asdf'] + print asdf cmdline = "bash %s %s %s %s" % ( shscript, options['bamout'], options['bamout2'], options['input1'] ) elif (options['action'] == "pileup"): #cmdline = "perl /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )