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comparison sam_pileup.py @ 4:a3b4ad6858ff draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_pileup commit 8301d37348be25a038b3c63b049b1178d05f5003"
author devteam
date Thu, 06 Feb 2020 07:11:33 -0500
parents 890d97772e2a
children
comparison
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3:890d97772e2a 4:a3b4ad6858ff
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
12 -g, --index=g: Path of the indexed reference genome
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':
86 if not os.path.exists( "%s.fai" % options.index ):
87 raise Exception, "Indexed genome %s not present, request it by reporting this error." % options.index
88 cmd = cmd % ( opts, options.index, tmpf0bam_name, options.output1 )
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__()