Mercurial > repos > zzhou > bamedit
diff bamedit.py @ 29:215f9e9855e6 draft
Uploaded
| author | zzhou |
|---|---|
| date | Mon, 26 Nov 2012 11:33:11 -0500 |
| parents | 4e70455b49e6 |
| children | 903000ebc92c |
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--- a/bamedit.py Mon Nov 26 11:31:41 2012 -0500 +++ b/bamedit.py Mon Nov 26 11:33:11 2012 -0500 @@ -19,10 +19,10 @@ 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'] ) - cmdline = "bash $SCRIPT_PATH//split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] ) + cmdline = "bash $SCRIPT_PATH\/split.sh %s %s %s" % ( 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'] ) - cmdline = "perl $SCRIPT_PATH//pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] ) + cmdline = "perl $SCRIPT_PATH\/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] ) elif (options['action'] == "filter"): cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] )