Mercurial > repos > jjohnson > shear
comparison shear_wrapper.py @ 0:65255beda972
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| author | jjohnson |
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| date | Fri, 08 Nov 2013 16:23:10 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:65255beda972 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import optparse, os, shutil, subprocess, sys, tempfile, os.path | |
| 4 | |
| 5 def stop_err( msg, code ): | |
| 6 sys.stderr.write( '%s\n' % msg ) | |
| 7 sys.exit(code) | |
| 8 | |
| 9 def __main__(): | |
| 10 #Parse Command Line | |
| 11 parser = optparse.OptionParser() | |
| 12 parser.add_option( '-j', '--jar_path', dest='jar_path', help='Path to SHEAR.jar' ) | |
| 13 parser.add_option( '-C', '--command', dest='command', help='SHEAR command to run' ) | |
| 14 parser.add_option( '-p', '--prefix', dest='prefix', help='Prefix for all generated files. Required.' ) | |
| 15 parser.add_option( '-b', '--bam', dest='bam', help='BAM alignment file containing the input sequences to the assembly.' ) | |
| 16 parser.add_option( '-B', '--bai', dest='bai', help='BAM index file (.bai)' ) | |
| 17 parser.add_option( '-f', '--fasta_reference', dest='fasta', help='The reference sequence fasta file' ) | |
| 18 parser.add_option( '-F', '--fasta_index', dest='fai', help='The .fai index file for the reference sequence fasta' ) | |
| 19 parser.add_option( '-t', '--twobit', dest='twobit', help='The .2bit encoding of the reference sequence fasta generated by faToTwoBit' ) | |
| 20 parser.add_option( '-i', '--bwa_index', dest='bwa_index', help='The bwa index of the reference sequence' ) | |
| 21 parser.add_option( '-R', '--report', dest='report', help='The SHEAR output report' ) | |
| 22 parser.add_option( '-s', '--sdi', dest='sdi', help='The SHEAR sdi input from the SHEAR sv command' ) | |
| 23 parser.add_option( '-o', '--output', dest='output', help='The SHEAR output assembly fasta file' ) | |
| 24 parser.add_option( '-D', '--svidx_dir', dest='svidx_dir', help='The SHEAR output assembly fasta file' ) | |
| 25 parser.add_option( '-S', '--sv-only', dest='sv_only', action="store_true", help='SV Only prediction mode.' ) | |
| 26 parser.add_option( '-r', '--region', dest='region', help='Region of the input alignment to analyze' ) | |
| 27 (options, args) = parser.parse_args() | |
| 28 | |
| 29 def make_ref(src, dest, copy=False): | |
| 30 if copy: | |
| 31 shutil.copy( src, dest ) | |
| 32 else: | |
| 33 os.symlink( src, dest ) | |
| 34 | |
| 35 # output version # of tool | |
| 36 #try: | |
| 37 #except: | |
| 38 # sys.stdout.write( 'Could not determine BWA version\n' ) | |
| 39 if not options.jar_path: | |
| 40 stop_err('path to SHEAR.jar is required',1) | |
| 41 if options.command: | |
| 42 command = options.command | |
| 43 else: | |
| 44 stop_err('SHEAR command is required',1) | |
| 45 args = [ 'java','-jar' ] | |
| 46 args.append( options.jar_path ) | |
| 47 args.append( command ) | |
| 48 # Check required params for command | |
| 49 buffsize = 1048576 | |
| 50 copy_ref = True | |
| 51 prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref' | |
| 52 if command in ['sv']: | |
| 53 args.append( '-p' ) | |
| 54 args.append( prefix ) | |
| 55 if options.sv_only: | |
| 56 args.append('--sv-only') | |
| 57 if options.region: | |
| 58 args.append('-r') | |
| 59 args.append(options.region) | |
| 60 copy_ref = True # GATK has issue with symlinks for .fa and .fai | |
| 61 if options.svidx_dir and command in ['sv']: | |
| 62 if not os.path.isdir(options.svidx_dir): | |
| 63 os.makedirs(options.svidx_dir) | |
| 64 ref_prefix = os.path.join(options.svidx_dir,prefix) | |
| 65 copy_ref = True | |
| 66 else: | |
| 67 ref_prefix = os.path.join(os.getcwd(),prefix) | |
| 68 | |
| 69 if command in ['sv','assemble']: | |
| 70 ref_fasta = ref_prefix + '.fa' | |
| 71 ref_index = ref_fasta + '.fai' | |
| 72 if options.fasta: | |
| 73 make_ref( options.fasta, ref_fasta, copy=copy_ref ) | |
| 74 else: | |
| 75 stop_err('Reference fasta file is required',3) | |
| 76 # if reference fasta index is not supllied, generate it | |
| 77 if options.fai: | |
| 78 make_ref( options.fai, ref_index, copy=copy_ref ) | |
| 79 elif os.path.exists(options.fasta + '.fai'): | |
| 80 make_ref( options.fasta + '.fai', ref_index, copy=copy_ref ) | |
| 81 else: | |
| 82 # generate fasta fai index | |
| 83 cmd1 = 'samtools faidx %s' % (ref_fasta ) | |
| 84 try: | |
| 85 tmp_name = tempfile.NamedTemporaryFile(prefix='fai_', suffix='.err').name | |
| 86 tmp_stderr = open( tmp_name, 'wb' ) | |
| 87 proc = subprocess.Popen( args=cmd1, shell=True, stderr=tmp_stderr.fileno() ) | |
| 88 returncode = proc.wait() | |
| 89 tmp_stderr.close() | |
| 90 if returncode != 0: | |
| 91 stderr = '' | |
| 92 # get stderr, allowing for case where it's very large | |
| 93 tmp_stderr = open( tmp, 'rb' ) | |
| 94 try: | |
| 95 while True: | |
| 96 stderr += tmp_stderr.read( buffsize ) | |
| 97 if not stderr or len( stderr ) % buffsize != 0: | |
| 98 break | |
| 99 except OverflowError: | |
| 100 pass | |
| 101 raise Exception, stderr | |
| 102 except Exception, e: | |
| 103 stop_err( 'Error indexing reference sequence fasta file. ' + str( e ),5 ) | |
| 104 args.append( '-f' ) | |
| 105 args.append( ref_fasta ) | |
| 106 | |
| 107 if command in ['sv']: | |
| 108 if not options.bam: | |
| 109 stop_err('BAM alignment file is required',2) | |
| 110 | |
| 111 # if reference 2bit is not supplied, generate it | |
| 112 twobit = ref_prefix + '.2bit' | |
| 113 if options.twobit: | |
| 114 make_ref( options.twobit, twobit, copy=copy_ref ) | |
| 115 else: | |
| 116 # generate 2bit index | |
| 117 cmd1 = 'faToTwoBit %s %s' % (ref_fasta, twobit ) | |
| 118 try: | |
| 119 tmp_name = tempfile.NamedTemporaryFile(prefix='twobit_', suffix='.err').name | |
| 120 tmp_stderr = open( tmp_name, 'wb' ) | |
| 121 proc = subprocess.Popen( args=cmd1, shell=True, stderr=tmp_stderr.fileno() ) | |
| 122 returncode = proc.wait() | |
| 123 tmp_stderr.close() | |
| 124 if returncode != 0: | |
| 125 stderr = '' | |
| 126 # get stderr, allowing for case where it's very large | |
| 127 tmp_stderr = open( tmp, 'rb' ) | |
| 128 try: | |
| 129 while True: | |
| 130 stderr += tmp_stderr.read( buffsize ) | |
| 131 if not stderr or len( stderr ) % buffsize != 0: | |
| 132 break | |
| 133 except OverflowError: | |
| 134 pass | |
| 135 raise Exception, stderr | |
| 136 except Exception, e: | |
| 137 stop_err( 'Error indexing reference sequence fasta file. ' + str( e ),6 ) | |
| 138 args.append( '-t' ) | |
| 139 args.append( twobit ) | |
| 140 | |
| 141 # if bwa index is not supplied, generate it | |
| 142 bwa_index = ref_fasta | |
| 143 if options.bwa_index: | |
| 144 if copy_ref: | |
| 145 shutil.copytree(os.path.dirname(bwa_index),options.svidx_dir) | |
| 146 bwa_index = options.bwa_index | |
| 147 else: | |
| 148 ONE_GB = 2**30 | |
| 149 if os.stat( ref_fasta ).st_size <= ONE_GB: #use 1 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary | |
| 150 index_algorithm = 'is' | |
| 151 else: | |
| 152 index_algorithm = 'bwtsw' | |
| 153 cmd1 = 'bwa index -a %s %s' % ( index_algorithm, ref_fasta ) | |
| 154 try: | |
| 155 tmp_name = tempfile.NamedTemporaryFile(prefix='bwa_index_', suffix='.err').name | |
| 156 tmp_stderr = open( tmp_name, 'wb' ) | |
| 157 proc = subprocess.Popen( args=cmd1, shell=True, stderr=tmp_stderr.fileno() ) | |
| 158 returncode = proc.wait() | |
| 159 tmp_stderr.close() | |
| 160 if returncode != 0: | |
| 161 stderr = '' | |
| 162 # get stderr, allowing for case where it's very large | |
| 163 tmp_stderr = open( tmp, 'rb' ) | |
| 164 try: | |
| 165 while True: | |
| 166 stderr += tmp_stderr.read( buffsize ) | |
| 167 if not stderr or len( stderr ) % buffsize != 0: | |
| 168 break | |
| 169 except OverflowError: | |
| 170 pass | |
| 171 raise Exception, stderr | |
| 172 bwa_index = ref_fasta | |
| 173 except Exception, e: | |
| 174 # clean up temp dirs | |
| 175 stop_err( 'Error creating bwa index. ' + str( e ),7 ) | |
| 176 args.append( '-i' ) | |
| 177 args.append( bwa_index ) | |
| 178 | |
| 179 bam_file = os.path.join(os.getcwd(),prefix + '.bam') | |
| 180 bai_file = bam_file + '.bai' | |
| 181 if options.bam: | |
| 182 os.symlink( options.bam, bam_file ) | |
| 183 else: | |
| 184 stop_err('BAM alignment file is required',2) | |
| 185 # if bam index is not supplied, generate it | |
| 186 if options.bai: | |
| 187 os.symlink( options.bai, bai_file ) | |
| 188 elif os.path.exists(options.bam + '.bai'): | |
| 189 os.symlink( options.bam + '.bai', bai_file ) | |
| 190 else: | |
| 191 # generate bam index | |
| 192 cmd1 = 'samtools index %s %s' % (bam_file, bai_file ) | |
| 193 try: | |
| 194 tmp_name = tempfile.NamedTemporaryFile(prefix='bai_', suffix='.err').name | |
| 195 tmp_stderr = open( tmp_name, 'wb' ) | |
| 196 proc = subprocess.Popen( args=cmd1, shell=True, stderr=tmp_stderr.fileno() ) | |
| 197 returncode = proc.wait() | |
| 198 tmp_stderr.close() | |
| 199 if returncode != 0: | |
| 200 stderr = '' | |
| 201 # get stderr, allowing for case where it's very large | |
| 202 tmp_stderr = open( tmp, 'rb' ) | |
| 203 try: | |
| 204 while True: | |
| 205 stderr += tmp_stderr.read( buffsize ) | |
| 206 if not stderr or len( stderr ) % buffsize != 0: | |
| 207 break | |
| 208 except OverflowError: | |
| 209 pass | |
| 210 raise Exception, stderr | |
| 211 except Exception, e: | |
| 212 stop_err( 'Error indexing BAM alignment file. ' + str( e ),4) | |
| 213 args.append( '-b' ) | |
| 214 args.append( bam_file ) | |
| 215 | |
| 216 if command in ['assemble']: | |
| 217 if not options.sdi or not options.output: | |
| 218 stop_err('SHEAR .sdi file and output file are required for assemble',2) | |
| 219 args.append( '-s' ) | |
| 220 args.append( options.sdi ) | |
| 221 args.append( '-o' ) | |
| 222 args.append( options.output ) | |
| 223 | |
| 224 # Run SHEAR command | |
| 225 print >> sys.stdout, "%s" % ' '.join(args) | |
| 226 try: | |
| 227 proc = subprocess.Popen( args=args, shell=False ) | |
| 228 returncode = proc.wait() | |
| 229 if returncode != 0: | |
| 230 stop_err( 'Error running SHEAR ' + command, returncode ) | |
| 231 except Exception, e: | |
| 232 # clean up temp dirs | |
| 233 stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 ) | |
| 234 | |
| 235 if __name__=="__main__": __main__() | |
| 236 |