Mercurial > repos > ziru-zhou > bamedit
comparison bamedit.py @ 0:2a516d8a4ff9 draft
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| author | ziru-zhou |
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| date | Tue, 18 Dec 2012 09:19:42 -0500 |
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| -1:000000000000 | 0:2a516d8a4ff9 |
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| 1 #purpose: python wrapper for bamedit tool | |
| 2 #author: Ziru Zhou | |
| 3 #date: October, 2012 | |
| 4 | |
| 5 import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip | |
| 6 from galaxy import eggs | |
| 7 import pkg_resources | |
| 8 pkg_resources.require( "simplejson" ) | |
| 9 import simplejson | |
| 10 | |
| 11 CHUNK_SIZE = 1024 | |
| 12 | |
| 13 def main(): | |
| 14 options = simplejson.load( open( sys.argv[1] ) ) | |
| 15 script_path = sys.argv[2] | |
| 16 | |
| 17 if(options['action'] == "merge"): | |
| 18 cmdline = "samtools merge %s %s %s" % ( options['bamout'], options['input1'], options['input2'] ) | |
| 19 if('input3' in options): | |
| 20 cmdline = "samtools merge %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] ) | |
| 21 elif (options['action'] == "split"): | |
| 22 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] ) | |
| 23 cmdline = "bash %s/split.sh %s %s %s" % (script_path, options['bamout'], options['bamout2'], options['input1'] ) | |
| 24 elif (options['action'] == "pileup"): | |
| 25 #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'] ) | |
| 26 cmdline = "perl %s/pileup.pl %s %s %s %s %s" % (script_path, options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] ) | |
| 27 elif (options['action'] == "filter"): | |
| 28 cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] ) | |
| 29 | |
| 30 #create tempdir for output files and stderr reports | |
| 31 tmp_dir = tempfile.mkdtemp() | |
| 32 stderr_name = tempfile.NamedTemporaryFile().name | |
| 33 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) | |
| 34 proc.wait() | |
| 35 | |
| 36 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup | |
| 37 if proc.returncode: | |
| 38 stderr_f = open( stderr_name ) | |
| 39 while True: | |
| 40 chunk = stderr_f.read( CHUNK_SIZE ) | |
| 41 if not chunk: | |
| 42 stderr_f.close() | |
| 43 break | |
| 44 sys.stderr.write( chunk ) | |
| 45 | |
| 46 if __name__ == "__main__": main() |