Mercurial > repos > saket-choudhary > eqtl_tools

annotate panama_run.py @ 2:c72dac728b06

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Adding tool dependency
author Saket Choudhary<saketkc@gmail.com>
date Sun, 16 Jun 2013 17:02:23 +0530
parents 7265ecc0f879
children
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1
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1 #!/usr/bin/env python
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2 """
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3 Run panama on expression and snp data
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4 usage: panama_run.py [options]
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5 --exp_data: Expression data CSV file
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6 --snp_data: SNP data file
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7 --output1: Output CSV dataset
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8 """
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9
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10 import optparse, os, sys, subprocess, tempfile, shutil
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11 from galaxy import eggs
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12 import pkg_resources; pkg_resources.require( "bx-python" )
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13 from bx.cookbook import doc_optparse
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14 from galaxy import util
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15
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16 def stop_err( msg ):
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17 sys.stderr.write( '%s\n' % msg )
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18 sys.exit()
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19
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20
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21
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22 def __main__():
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23 #Parse Command Line
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24 parser = optparse.OptionParser()
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25 parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset')
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26 parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' )
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27 parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' )
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28 ( options, args ) = parser.parse_args()
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29
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30 try:
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31 tmp_dir = tempfile.mkdtemp()
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32 panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv")
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33 command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir)
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34 print command
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35 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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36 tmp_stderr = open( tmp, 'wb' )
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37 proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() )
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38 returncode = proc.wait()
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39 tmp_stderr.close()
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40 # get stderr, allowing for case where it's very large
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41 tmp_stderr = open( tmp, 'rb' )
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42 stderr = ''
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43 buffsize = 1048576
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44 try:
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45 while True:
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46 stderr += tmp_stderr.read( buffsize )
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47 if not stderr or len( stderr ) % buffsize != 0:
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48 break
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49 except OverflowError:
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50 pass
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51 tmp_stderr.close()
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52 if returncode != 0:
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53 raise Exception, stderr
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54 except Exception, e:
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55 #clean up temp files
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56 print e
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57 if os.path.exists( tmp_dir ):
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58 shutil.rmtree( tmp_dir )
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59 stop_err( 'Error opening panama')
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60 # Move tmp_aligns_file_name to our output dataset location
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61 shutil.move( panama_output_file_name, options.output1 )
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62 #clean up temp files
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63 if os.path.exists( tmp_dir ):
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64 shutil.rmtree( tmp_dir )
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65 # check that there are results in the output file
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66 if os.path.getsize( options.output1 ) > 0:
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67 sys.stdout.write( 'PANAM results generated' )
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68 else:
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69 stop_err( 'Error generating PANAMA results' )
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70
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71 if __name__=="__main__": __main__()