Mercurial > repos > devteam > sam_pileup
annotate sam_pileup.py @ 1:efd77ef84903 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:30:34 -0400 |
| parents | cb3966035753 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 | |
| 3 """ | |
| 4 Creates a pileup file from a bam file and a reference. | |
| 5 | |
| 6 usage: %prog [options] | |
| 7 -p, --input1=p: bam file | |
| 8 -o, --output1=o: Output pileup | |
| 9 -R, --ref=R: Reference file type | |
| 10 -n, --ownFile=n: User-supplied fasta reference file | |
| 11 -b, --bamIndex=b: BAM index file | |
|
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efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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12 -g, --index=g: Path of the indexed reference genome |
| 0 | 13 -s, --lastCol=s: Print the mapping quality as the last column |
| 14 -i, --indels=i: Only output lines containing indels | |
| 15 -M, --mapCap=M: Cap mapping quality | |
| 16 -c, --consensus=c: Call the consensus sequence using MAQ consensu model | |
| 17 -T, --theta=T: Theta paramter (error dependency coefficient) | |
| 18 -N, --hapNum=N: Number of haplotypes in sample | |
| 19 -r, --fraction=r: Expected fraction of differences between a pair of haplotypes | |
| 20 -I, --phredProb=I: Phred probability of an indel in sequencing/prep | |
| 21 | |
| 22 """ | |
| 23 | |
| 24 import os, shutil, subprocess, sys, tempfile | |
| 25 from galaxy import eggs | |
| 26 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 27 from bx.cookbook import doc_optparse | |
| 28 | |
| 29 def stop_err( msg ): | |
| 30 sys.stderr.write( '%s\n' % msg ) | |
| 31 sys.exit() | |
| 32 | |
| 33 def __main__(): | |
| 34 #Parse Command Line | |
| 35 options, args = doc_optparse.parse( __doc__ ) | |
| 36 # output version # of tool | |
| 37 try: | |
| 38 tmp = tempfile.NamedTemporaryFile().name | |
| 39 tmp_stdout = open( tmp, 'wb' ) | |
| 40 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout ) | |
| 41 tmp_stdout.close() | |
| 42 returncode = proc.wait() | |
| 43 stdout = None | |
| 44 for line in open( tmp_stdout.name, 'rb' ): | |
| 45 if line.lower().find( 'version' ) >= 0: | |
| 46 stdout = line.strip() | |
| 47 break | |
| 48 if stdout: | |
| 49 sys.stdout.write( 'Samtools %s\n' % stdout ) | |
| 50 else: | |
| 51 raise Exception | |
| 52 except: | |
| 53 sys.stdout.write( 'Could not determine Samtools version\n' ) | |
| 54 #prepare file names | |
| 55 tmpDir = tempfile.mkdtemp() | |
| 56 tmpf0 = tempfile.NamedTemporaryFile( dir=tmpDir ) | |
| 57 tmpf0_name = tmpf0.name | |
| 58 tmpf0.close() | |
| 59 tmpf0bam_name = '%s.bam' % tmpf0_name | |
| 60 tmpf0bambai_name = '%s.bam.bai' % tmpf0_name | |
| 61 tmpf1 = tempfile.NamedTemporaryFile( dir=tmpDir ) | |
| 62 tmpf1_name = tmpf1.name | |
| 63 tmpf1.close() | |
| 64 #link bam and bam index to working directory (can't move because need to leave original) | |
| 65 os.symlink( options.input1, tmpf0bam_name ) | |
| 66 os.symlink( options.bamIndex, tmpf0bambai_name ) | |
| 67 #get parameters for pileup command | |
| 68 if options.lastCol == 'yes': | |
| 69 lastCol = '-s' | |
| 70 else: | |
| 71 lastCol = '' | |
| 72 if options.indels == 'yes': | |
| 73 indels = '-i' | |
| 74 else: | |
| 75 indels = '' | |
| 76 opts = '%s %s -M %s' % ( lastCol, indels, options.mapCap ) | |
| 77 if options.consensus == 'yes': | |
| 78 opts += ' -c -T %s -N %s -r %s -I %s' % ( options.theta, options.hapNum, options.fraction, options.phredProb ) | |
| 79 #prepare basic pileup command | |
| 80 cmd = 'samtools pileup %s -f %s %s > %s' | |
| 81 try: | |
| 82 # have to nest try-except in try-finally to handle 2.4 | |
| 83 try: | |
| 84 #index reference if necessary and prepare pileup command | |
| 85 if options.ref == 'indexed': | |
|
1
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
86 if not os.path.exists( "%s.fai" % options.index ): |
|
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
87 raise Exception, "Indexed genome %s not present, request it by reporting this error." % options.index |
|
efd77ef84903
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
88 cmd = cmd % ( opts, options.index, tmpf0bam_name, options.output1 ) |
| 0 | 89 elif options.ref == 'history': |
| 90 os.symlink( options.ownFile, tmpf1_name ) | |
| 91 cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) | |
| 92 tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name | |
| 93 tmp_stderr = open( tmp, 'wb' ) | |
| 94 proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) | |
| 95 returncode = proc.wait() | |
| 96 tmp_stderr.close() | |
| 97 # get stderr, allowing for case where it's very large | |
| 98 tmp_stderr = open( tmp, 'rb' ) | |
| 99 stderr = '' | |
| 100 buffsize = 1048576 | |
| 101 try: | |
| 102 while True: | |
| 103 stderr += tmp_stderr.read( buffsize ) | |
| 104 if not stderr or len( stderr ) % buffsize != 0: | |
| 105 break | |
| 106 except OverflowError: | |
| 107 pass | |
| 108 tmp_stderr.close() | |
| 109 #did index succeed? | |
| 110 if returncode != 0: | |
| 111 raise Exception, 'Error creating index file\n' + stderr | |
| 112 cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 ) | |
| 113 #perform pileup command | |
| 114 tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name | |
| 115 tmp_stderr = open( tmp, 'wb' ) | |
| 116 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) | |
| 117 returncode = proc.wait() | |
| 118 tmp_stderr.close() | |
| 119 #did it succeed? | |
| 120 # get stderr, allowing for case where it's very large | |
| 121 tmp_stderr = open( tmp, 'rb' ) | |
| 122 stderr = '' | |
| 123 buffsize = 1048576 | |
| 124 try: | |
| 125 while True: | |
| 126 stderr += tmp_stderr.read( buffsize ) | |
| 127 if not stderr or len( stderr ) % buffsize != 0: | |
| 128 break | |
| 129 except OverflowError: | |
| 130 pass | |
| 131 tmp_stderr.close() | |
| 132 if returncode != 0: | |
| 133 raise Exception, stderr | |
| 134 except Exception, e: | |
| 135 stop_err( 'Error running Samtools pileup tool\n' + str( e ) ) | |
| 136 finally: | |
| 137 #clean up temp files | |
| 138 if os.path.exists( tmpDir ): | |
| 139 shutil.rmtree( tmpDir ) | |
| 140 # check that there are results in the output file | |
| 141 if os.path.getsize( options.output1 ) > 0: | |
| 142 sys.stdout.write( 'Converted BAM to pileup' ) | |
| 143 else: | |
| 144 stop_err( 'The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings.' ) | |
| 145 | |
| 146 if __name__ == "__main__" : __main__() |