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comparison tools/sr_mapping/srma_wrapper.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Runs SRMA on a SAM/BAM file;
5 TODO: more documentation
6
7 usage: srma_wrapper.py [options]
8
9 See below for options
10 """
11
12 import optparse, os, shutil, subprocess, sys, tempfile
13
14 def stop_err( msg ):
15 sys.stderr.write( '%s\n' % msg )
16 sys.exit()
17
18 def parseRefLoc( refLoc, refUID ):
19 for line in open( refLoc ):
20 if not line.startswith( '#' ):
21 fields = line.strip().split( '\t' )
22 if len( fields ) >= 3:
23 if fields[0] == refUID:
24 return fields[1]
25 return None
26
27 def __main__():
28 #Parse Command Line
29 parser = optparse.OptionParser()
30 parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' )
31 parser.add_option( '-u', '--refUID', dest='refUID', help='The pre-index reference genome unique Identifier' )
32 parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' )
33 parser.add_option( '-i', '--input', dest='input', help='The SAM/BAM input file' )
34 parser.add_option( '-I', '--inputIndex', dest='inputIndex', help='The SAM/BAM input index file' )
35 parser.add_option( '-o', '--output', dest='output', help='The SAM/BAM output file' )
36 parser.add_option( '-O', '--offset', dest='offset', help='The alignment offset' )
37 parser.add_option( '-Q', '--minMappingQuality', dest='minMappingQuality', help='The minimum mapping quality' )
38 parser.add_option( '-P', '--minAlleleProbability', dest='minAlleleProbability', help='The minimum allele probability conditioned on coverage (for the binomial quantile).' )
39 parser.add_option( '-C', '--minAlleleCoverage', dest='minAlleleCoverage', help='The minimum haploid coverage for the consensus' )
40 parser.add_option( '-R', '--range', dest='range', help='A range to examine' )
41 parser.add_option( '-c', '--correctBases', dest='correctBases', help='Correct bases ' )
42 parser.add_option( '-q', '--useSequenceQualities', dest='useSequenceQualities', help='Use sequence qualities ' )
43 parser.add_option( '-M', '--maxHeapSize', dest='maxHeapSize', help='The maximum number of nodes on the heap before re-alignment is ignored' )
44 parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
45 parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
46 parser.add_option( '-j', '--jarBin', dest='jarBin', default='', help='The path to where jars are stored' )
47 parser.add_option( '-f', '--jarFile', dest='jarFile', help='The file name of the jar file to use')
48 (options, args) = parser.parse_args()
49
50 # make temp directory for srma
51 tmp_dir = tempfile.mkdtemp()
52 buffsize = 1048576
53
54 # set up reference filenames
55 reference_filepath_name = None
56 # need to create SRMA dict and Samtools fai files for custom genome
57 if options.fileSource == 'history':
58 try:
59 reference_filepath = tempfile.NamedTemporaryFile( dir=tmp_dir, suffix='.fa' )
60 reference_filepath_name = reference_filepath.name
61 reference_filepath.close()
62 fai_filepath_name = '%s.fai' % reference_filepath_name
63 dict_filepath_name = reference_filepath_name.replace( '.fa', '.dict' )
64 os.symlink( options.ref, reference_filepath_name )
65 # create fai file using Samtools
66 index_fai_cmd = 'samtools faidx %s' % reference_filepath_name
67 try:
68 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
69 tmp_stderr = open( tmp, 'wb' )
70 proc = subprocess.Popen( args=index_fai_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
71 returncode = proc.wait()
72 tmp_stderr.close()
73 # get stderr, allowing for case where it's very large
74 tmp_stderr = open( tmp, 'rb' )
75 stderr = ''
76 try:
77 while True:
78 stderr += tmp_stderr.read( buffsize )
79 if not stderr or len( stderr ) % buffsize != 0:
80 break
81 except OverflowError:
82 pass
83 tmp_stderr.close()
84 if returncode != 0:
85 raise Exception, stderr
86 except Exception, e:
87 # clean up temp dir
88 if os.path.exists( tmp_dir ):
89 shutil.rmtree( tmp_dir )
90 stop_err( 'Error creating Samtools index for custom genome file: %s\n' % str( e ) )
91 # create dict file using SRMA
92 dict_cmd = 'java -cp "%s" net.sf.picard.sam.CreateSequenceDictionary R=%s O=%s' % ( os.path.join( options.jarBin, options.jarFile ), reference_filepath_name, dict_filepath_name )
93 try:
94 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
95 tmp_stderr = open( tmp, 'wb' )
96 proc = subprocess.Popen( args=dict_cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
97 returncode = proc.wait()
98 tmp_stderr.close()
99 # get stderr, allowing for case where it's very large
100 tmp_stderr = open( tmp, 'rb' )
101 stderr = ''
102 try:
103 while True:
104 stderr += tmp_stderr.read( buffsize )
105 if not stderr or len( stderr ) % buffsize != 0:
106 break
107 except OverflowError:
108 pass
109 tmp_stderr.close()
110 if returncode != 0:
111 raise Exception, stderr
112 except Exception, e:
113 # clean up temp dir
114 if os.path.exists( tmp_dir ):
115 shutil.rmtree( tmp_dir )
116 stop_err( 'Error creating index for custom genome file: %s\n' % str( e ) )
117 except Exception, e:
118 # clean up temp dir
119 if os.path.exists( tmp_dir ):
120 shutil.rmtree( tmp_dir )
121 stop_err( 'Problem handling SRMA index (dict file) for custom genome file: %s\n' % str( e ) )
122 # using built-in dict/index files
123 else:
124 if options.ref:
125 reference_filepath_name = options.ref
126 else:
127 reference_filepath_name = parseRefLoc( options.refLocation, options.refUID )
128 if reference_filepath_name is None:
129 raise ValueError( 'A valid genome reference was not provided.' )
130
131 # set up aligning and generate aligning command options
132 if options.params == 'pre_set':
133 srma_cmds = ''
134 else:
135 if options.useSequenceQualities == 'true':
136 useSequenceQualities = 'true'
137 else:
138 useSequenceQualities = 'false'
139 ranges = 'null'
140 if options.range == 'None':
141 range = 'null'
142 else:
143 range = options.range
144 srma_cmds = "OFFSET=%s MIN_MAPQ=%s MINIMUM_ALLELE_PROBABILITY=%s MINIMUM_ALLELE_COVERAGE=%s RANGES=%s RANGE=%s CORRECT_BASES=%s USE_SEQUENCE_QUALITIES=%s MAX_HEAP_SIZE=%s" % ( options.offset, options.minMappingQuality, options.minAlleleProbability, options.minAlleleCoverage, ranges, range, options.correctBases, options.useSequenceQualities, options.maxHeapSize )
145
146 # perform alignments
147 buffsize = 1048576
148 try:
149 #symlink input bam and index files due to the naming conventions required by srma here
150 input_bam_filename = os.path.join( tmp_dir, '%s.bam' % os.path.split( options.input )[-1] )
151 os.symlink( options.input, input_bam_filename )
152 input_bai_filename = "%s.bai" % os.path.splitext( input_bam_filename )[0]
153 os.symlink( options.inputIndex, input_bai_filename )
154
155 #create a temp output name, ending in .bam due to required naming conventions? unkown if required
156 output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] )
157 # generate commandline
158 cmd = 'java -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds )
159
160 # need to nest try-except in try-finally to handle 2.4
161 try:
162 try:
163 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
164 tmp_stderr = open( tmp, 'wb' )
165 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
166 returncode = proc.wait()
167 tmp_stderr.close()
168 # get stderr, allowing for case where it's very large
169 tmp_stderr = open( tmp, 'rb' )
170 stderr = ''
171 try:
172 while True:
173 stderr += tmp_stderr.read( buffsize )
174 if not stderr or len( stderr ) % buffsize != 0:
175 break
176 except OverflowError:
177 pass
178 tmp_stderr.close()
179 if returncode != 0:
180 raise Exception, stderr
181 except Exception, e:
182 raise Exception, 'Error executing SRMA. ' + str( e )
183 # move file from temp location (with .bam name) to provided path
184 shutil.move( output_bam_filename, options.output )
185 # check that there are results in the output file
186 if os.path.getsize( options.output ) <= 0:
187 raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
188 except Exception, e:
189 stop_err( 'The re-alignment failed.\n' + str( e ) )
190 finally:
191 # clean up temp dir
192 if os.path.exists( tmp_dir ):
193 shutil.rmtree( tmp_dir )
194
195 if __name__=="__main__": __main__()