Mercurial > repos > modencode-dcc > bamedit
changeset 13:1ceeba7b95a4 draft
Uploaded
| author | modencode-dcc |
|---|---|
| date | Mon, 21 Jan 2013 13:33:01 -0500 |
| parents | 7a51d316635a |
| children | feaf4d152d6b |
| files | bamedit.py |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/bamedit.py Fri Jan 18 15:55:46 2013 -0500 +++ b/bamedit.py Mon Jan 21 13:33:01 2013 -0500 @@ -12,6 +12,7 @@ def main(): options = simplejson.load( open( sys.argv[1] ) ) + script_path = sys.argv[2] #experiment_name = '_'.join( options['bamout'] ) @@ -20,9 +21,9 @@ 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_tools/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] ) + cmdline = "bash %s/split.sh %s %s %s" % ( script_path, options['bamout'], options['bamout2'], options['input1'] ) elif (options['action'] == "pileup"): - cmdline = "perl /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/bamedit/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] ) + cmdline = "perl %s/pileup.pl %s %s %s %s %s" % ( script_path, 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'] )