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comparison shear_wrapper.py @ 6:0158f7356ffd

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Add new outputs and params to shear_sv.xml for version 2.3
author Jim Johnson <jj@umn.edu>
date Mon, 21 Oct 2013 08:54:58 -0500
parents a82400332451
children 8fac6c7d32fd
comparison
equal deleted inserted replaced
5:aaaa5a071ff0 6:0158f7356ffd
16 parser.add_option( '-B', '--bai', dest='bai', help='BAM index file (.bai)' ) 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' ) 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' ) 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' ) 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' ) 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' ) 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' ) 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' ) 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' ) 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' )
25 (options, args) = parser.parse_args() 27 (options, args) = parser.parse_args()
26 28
27 def make_ref(src, dest, copy=False): 29 def make_ref(src, dest, copy=False):
28 if copy: 30 if copy:
29 shutil.copy( src, dest ) 31 shutil.copy( src, dest )
48 copy_ref = False 50 copy_ref = False
49 prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref' 51 prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref'
50 if command in ['sv']: 52 if command in ['sv']:
51 args.append( '-p' ) 53 args.append( '-p' )
52 args.append( prefix ) 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)
53 if options.svidx_dir and command in ['sv']: 60 if options.svidx_dir and command in ['sv']:
54 if not os.path.isdir(options.svidx_dir): 61 if not os.path.isdir(options.svidx_dir):
55 os.makedirs(options.svidx_dir) 62 os.makedirs(options.svidx_dir)
56 ref_prefix = os.path.join(options.svidx_dir,prefix) 63 ref_prefix = os.path.join(options.svidx_dir,prefix)
57 copy_ref = True 64 copy_ref = True
218 try: 225 try:
219 proc = subprocess.Popen( args=args, shell=False ) 226 proc = subprocess.Popen( args=args, shell=False )
220 returncode = proc.wait() 227 returncode = proc.wait()
221 if returncode != 0: 228 if returncode != 0:
222 stop_err( 'Error running SHEAR ' + command, returncode ) 229 stop_err( 'Error running SHEAR ' + command, returncode )
223 if command in ['sv']:
224 report_path = os.path.join(os.getcwd(),prefix + '.report')
225 if os.path.exists(report_path):
226 if options.report:
227 shutil.copy(report_path,options.report)
228 else:
229 raise Exception, 'no report file'
230 sdi_path = os.path.join(os.getcwd(),prefix + '.sdi')
231 if os.path.exists(sdi_path):
232 if options.sdi:
233 shutil.copy(sdi_path,options.sdi)
234 else:
235 raise Exception, 'no sdi file'
236 except Exception, e: 230 except Exception, e:
237 # clean up temp dirs 231 # clean up temp dirs
238 stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 ) 232 stop_err( 'Error running SHEAR %s %s' % (command,str(e)),9 )
239 233
240 if __name__=="__main__": __main__() 234 if __name__=="__main__": __main__()