tmap_wrapper: tmap_wrapper_0.3.3/tmap

annotate tmap_wrapper_0.3.3/tmap_wrapper.py @ 2:e2640d81157a default tip

* moving to TMAP 0.3.3

author	Nils Homer <nilshomer@gmail.com>
date	Sun, 26 Feb 2012 20:28:27 -0500
parents	tmap_wrapper_0.0.19/tmap_wrapper.py@de2efe4dda3f
children

rev	line source
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	1 #!/usr/bin/env python
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	2
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	3 # TODO
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	4 # - map1/map2/map3 specific options
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	5
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	6 """
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	7 Runs TMAP on Ion Torrent data.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	8 Produces a SAM file containing the mappings.
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	9 Works with TMAP version 0.3.3 or higher.
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	10
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	11 usage: tmap_wrapper.py [options]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	12 --threads: The number of threads to use
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	13 --ref: The reference genome to use or index
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	14 --input: The input FASTQ/SFF file to use for the mapping
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	15 --inputtype: The input type (FASTQ/SFF)
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	16 --output: The file to save the output (SAM format)
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	17 --params: Parameter setting to use (pre_set or full)
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	18 --fileSource: Whether to use a previously indexed reference sequence or one from history (indexed or history)
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	19 --algorithm: The algorithm (ex. mapall, map1, map2, map3, map4, ...)
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	20 --globalOptions: The global options
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	21 --flowspaceOptions: The flowspace options
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	22 --pairingOptions: The pairing options
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	23 --algorithmOptions: The algorithm options
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	24 --suppressHeader: Suppress header
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	25 --dbkey: Dbkey for reference genome
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	26 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	27 """
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	28
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	29 import optparse, os, shutil, subprocess, sys, tempfile
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	30
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	31 def stop_err( msg ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	32 sys.stderr.write( '%s\n' % msg )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	33 sys.exit()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	34
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	35 def __main__():
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	36 #Parse Command Line
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	37 parser = optparse.OptionParser()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	38 # Global options
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	39 parser.add_option( '--threads', dest='threads', help='The number of threads to use' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	40 parser.add_option( '--ref', dest='ref', help='The reference genome to use or index' )
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	41 parser.add_option( '--input', dest='input', help='The input file to use for the mapping' )
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	42 parser.add_option( '--inputtype', dest='inputtype', help='The input file type' )
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	43 parser.add_option( '--output', dest='output', help='The file to save the output (SAM format)' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	44 parser.add_option( '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	45 parser.add_option( '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	46 parser.add_option( '--algorithm', dest='algorithm', help='The algorithm (ex. mapall, map1, map2, map3, map4, ...)')
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	47 parser.add_option( '--globalOptions', dest='globalOptions', help='The global options ' )
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	48 parser.add_option( '--flowspaceOptions', dest='flowspaceOptions', help='The flowspace options' )
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	49 parser.add_option( '--pairingOptions', dest='pairingOptions', help='The pairing options' )
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	50 parser.add_option( '--algorithmOptions', dest='algorithmOptions', help='The algorithm options' )
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	51 parser.add_option( '--suppressHeader', dest='suppressHeader', help='Suppress header' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	52 parser.add_option( '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	53 parser.add_option( '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	54
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	55 # parse the options
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	56 (options, args) = parser.parse_args()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	57
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	58 # output version # of tool
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	59 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	60 tmp = tempfile.NamedTemporaryFile().name
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	61 tmp_stdout = open( tmp, 'wb' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	62 proc = subprocess.Popen( args='tmap --version 2>&1', shell=True, stdout=tmp_stdout )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	63 tmp_stdout.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	64 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	65 stdout = None
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	66 for line in open( tmp_stdout.name, 'rb' ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67 if line.lower().find( 'version' ) >= 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	68 stdout = line.strip()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	69 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	70 if stdout:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	71 sys.stdout.write( 'TMAP %s\n' % stdout )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	72 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	73 raise Exception
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	74 except:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	75 sys.stdout.write( 'Could not determine TMAP version\n' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	76
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	77 # make temp directory for placement of indices
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	78 tmp_index_dir = tempfile.mkdtemp()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	79 tmp_dir = tempfile.mkdtemp()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	80
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	81 # index if necessary
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	82 if options.fileSource == 'history' and not options.do_not_build_index:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	83 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	84 ref_file_name = ref_file.name
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	85 ref_file.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	86 os.symlink( options.ref, ref_file_name )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87 cmd1 = 'tmap index -f %s -v ' % ( ref_file_name )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	88 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	89 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	90 tmp_stderr = open( tmp, 'wb' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	91 proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	92 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	93 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	94 # get stderr, allowing for case where it's very large
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	95 tmp_stderr = open( tmp, 'rb' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	96 stderr = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	97 buffsize = 1048576
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	98 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	99 while True:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	100 stderr += tmp_stderr.read( buffsize )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	101 if not stderr or len( stderr ) % buffsize != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	102 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 except OverflowError:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	104 pass
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	105 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 if returncode != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	107 raise Exception, stderr
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 except Exception, e:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	109 # clean up temp dirs
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	110 if os.path.exists( tmp_index_dir ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	111 shutil.rmtree( tmp_index_dir )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	112 if os.path.exists( tmp_dir ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	113 shutil.rmtree( tmp_dir )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 stop_err( 'Error indexing reference sequence. ' + str( e ) )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116 ref_file_name = options.ref
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	117
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	118 # set up mapping and generate mapping command options
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119 if options.params == 'pre_set':
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	120 options.algorithm = 'mapall'
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	121 options.flowspaceOptions = ''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	122 options.pairingOptions = ''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	123 options.algorithmOptions = 'stage1 map1 map2 map3'
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	124
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125 #mapping_cmds
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 # prepare actual mapping and generate mapping commands
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	127 cmd = 'tmap %s -f %s -r %s -i %s -n %s %s %s %s > %s' % \
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	128 ( options.algorithm, options.ref, options.input, options.inputtype, \
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	129 options.threads, options.flowspaceOptions, \
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	130 options.pairingOptions, options.algorithmOptions, options.output )
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	131 # perform alignments
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	132 buffsize = 1048576
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	133 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	134 # need to nest try-except in try-finally to handle 2.4
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	135 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	136 # align
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	137 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	138 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	139 tmp_stderr = open( tmp, 'wb' )
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	140 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	141 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	142 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	143 # get stderr, allowing for case where it's very large
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	144 tmp_stderr = open( tmp, 'rb' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	145 stderr = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	146 try:
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	147 stderr += cmd + '\n'
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	148 while True:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	149 stderr += tmp_stderr.read( buffsize )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	150 if not stderr or len( stderr ) % buffsize != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	151 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	152 except OverflowError:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	153 pass
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	154 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	155 if returncode != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	156 raise Exception, stderr
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	157 except Exception, e:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	158 raise Exception, 'Error mapping sequence. ' + str( e )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	159 # remove header if necessary
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	160 if options.suppressHeader == 'true':
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	161 tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	162 tmp_out_name = tmp_out.name
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	163 tmp_out.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	164 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	165 shutil.move( options.output, tmp_out_name )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	166 except Exception, e:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	167 raise Exception, 'Error moving output file before removing headers. ' + str( e )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	168 fout = file( options.output, 'w' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	169 for line in file( tmp_out.name, 'r' ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	170 if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	171 fout.write( line )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	172 fout.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	173 # check that there are results in the output file
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	174 if os.path.getsize( options.output ) > 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	175 sys.stdout.write( 'TMAP completed' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	176 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	177 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.'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	178 except Exception, e:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	179 stop_err( 'The alignment failed.\n' + str( e ) )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	180 finally:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	181 # clean up temp dir
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	182 if os.path.exists( tmp_index_dir ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	183 shutil.rmtree( tmp_index_dir )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	184 if os.path.exists( tmp_dir ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	185 shutil.rmtree( tmp_dir )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	186
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	187 if __name__=="__main__": __main__()

Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.3.3/tmap_wrapper.py @ 2:e2640d81157a default tip