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4
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1 #purpose: python wrapper for bamedit tool
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2 #author: Ziru Zhou
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3 #date: October, 2012
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4
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5 import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
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6 from galaxy import eggs
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7 import pkg_resources
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8 pkg_resources.require( "simplejson" )
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9 import simplejson
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10
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11 CHUNK_SIZE = 1024
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12
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13 def main():
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14 options = simplejson.load( open( sys.argv[1] ) )
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18
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15
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39
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16 shscript = options['path']
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31
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17 plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
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30
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18 print shscript
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4
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19 if(options['action'] == "merge"):
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20 cmdline = "samtools merge %s %s %s" % ( options['bamout'], options['input1'], options['input2'] )
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21 if('input3' in options):
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22 cmdline = "samtools merge %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] )
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23 elif (options['action'] == "split"):
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18
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24 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
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30
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25 cmdline = "bash %s %s %s %s" % ( shscript, options['bamout'], options['bamout2'], options['input1'] )
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4
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26 elif (options['action'] == "pileup"):
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18
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27 #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'] )
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30
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28 cmdline = "perl %s %s %s %s %s %s" % ( plscript, options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
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4
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29 elif (options['action'] == "filter"):
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30 cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] )
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31
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32 #create tempdir for output files and stderr reports
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33 tmp_dir = tempfile.mkdtemp()
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34 stderr_name = tempfile.NamedTemporaryFile().name
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35 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
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36 proc.wait()
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37
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38 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
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39 if proc.returncode:
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40 stderr_f = open( stderr_name )
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41 while True:
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42 chunk = stderr_f.read( CHUNK_SIZE )
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43 if not chunk:
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44 stderr_f.close()
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45 break
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46 sys.stderr.write( chunk )
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47
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48 if __name__ == "__main__": main()
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