tmap_wrapper: tmap_wrapper_0.0.19/tmap

annotate tmap_wrapper_0.0.19/tmap_wrapper.py @ 1:40ade4f81a30 default tip

Uploaded tool_data_table_conf.xml.sample

author	nate
date	Fri, 23 Sep 2011 14:53:08 -0400
parents	7cbfd271d207
children

rev	line source
0 7cbfd271d207 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
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	2
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	3 # TODO
7cbfd271d207 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
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	5
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	6 """
7cbfd271d207 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.
7cbfd271d207 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.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	9 Works with TMAP version 0.0.19 or higher.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	10
7cbfd271d207 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]
7cbfd271d207 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
7cbfd271d207 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
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	14 --fastq: The fastq file to use for the mapping
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	15 --output: The file to save the output (SAM format)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	16 --params: Parameter setting to use (pre_set or full)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	17 --fileSource: Whether to use a previously indexed reference sequence or one from history (indexed or history)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	18 --matchScore: The match score
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	19 --mismatchPenalty: The ismatch penalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	20 --gapOpenPenalty: The gap open penalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	21 --gapExtensPenalty: The gap extension penalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	22 --flowPenalty: The flow score penalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	23 --flowOrder: The flow order ([ACGT]{4+} or "sff")
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	24 --bandWidth: The band width
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	25 --globalMap: The soft-clipping type (0 - allow on the right and left, 1 - allow on the left, 2 - allow on the right, 3 - do not allow soft-clipping)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	26 --duplicateWindow: Remove duplicate alignments from different algorithms within this bp window (-1 to disable)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	27 --scoringThreshold: The score threshold divided by the match score
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	28 --queueSize: The queue size for the reads
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	29 --outputFilter: The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	30 --rgTag: The flag to specify RG tag(s) in the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	31 --rgTagID: The RG ID tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	32 --rgTagCN: The RG CN tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	33 --rgTagDS: The RG DS tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	34 --rgTagDT: The RG DT tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	35 --rgTagLB: The RG LB tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	36 --rgTagPI: The RG PI tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	37 --rgTagPL: The RG PL tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	38 --rgTagPU: The RG PU tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	39 --rgTagSM: The RG SM tag to add to the SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	40 --filterIndependently: Apply the output filter for each algorithm independently
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	41
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	42 --map1: Flag to run map1 in the first stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	43 --map1SeedLength: The k-mer length to seed CALs (-1 to disable)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	44 --map1SeedMismatches: The maximum number of mismatches in the seed
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	45 --map1SecondarySeedLength: The secondary seed length (-1 to disable)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	46 --map1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	47 --map1BaseError: The assumed per-base maximum error rate
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	48 --map1Mismatches: The maximum number of or (read length) fraction of mismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	49 --map1GapOpens: The maximum number of or (read length) fraction of indel starts
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	50 --map1GapExtensions: The maximum number of or (read length) fraction of indel extensions
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	51 --map1MaxCALsDeletion: The maximum number of CALs to extend a deletion
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	52 --map1EndIndels: Indels are not allowed within this number of bps from the end of the read
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	53 --map1MaxOptimalCALs: Stop searching when INT optimal CALs have been found
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	54 --map1MaxNodes: The maximum number of alignment nodes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	55
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	56 --map2: Flag to run map2 in the first stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	57 --map2Coefficient: The coefficient of length-threshold adjustment
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	58 --map2SeedIntervalSize: The maximum seeding interval size
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	59 --map2ZBest: Keep the z-best nodes during prefix trie traversal
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	60 --map2ReverseTrigger: The # seeds to trigger reverse alignment
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	61
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	62 --map3: Flag to run map3 in the first stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	63 --map3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	64 --map3SeedMaxHits: The maximum number of hits returned by a seed
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	65 --map3SeedWindow: The window of bases in which to group seeds
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	66 --map3HPEnumeration: The single homopolymer error difference for enumeration
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	68 --MAP1: Flag to run MAP1 in the second stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	69 --MAP1SeedLength: The k-mer length to seed CALs (-1 to disable)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	70 --MAP1SeedMismatches: The maximum number of mismatches in the seed
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	71 --MAP1SecondarySeedLength: The secondary seed length (-1 to disable)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	72 --MAP1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	73 --MAP1BaseError: The assumed per-base maximum error rate
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	74 --MAP1Mismatches: The maximum number of or (read length) fraction of mismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	75 --MAP1GapOpens: The maximum number of or (read length) fraction of indel starts
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	76 --MAP1GapExtensions: The maximum number of or (read length) fraction of indel extensions
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	77 --MAP1MaxCALsDeletion: The maximum number of CALs to extend a deletion
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	78 --MAP1EndIndels: Indels are not allowed within this number of bps from the end of the read
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	79 --MAP1MaxOptimalCALs: Stop searching when INT optimal CALs have been found
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	80 --MAP1MaxNodes: The maximum number of alignment nodes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	81
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	82 --MAP2: Flag to run MAP2 in the second stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	83 --MAP2Coefficient: The coefficient of length-threshold adjustment
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	84 --MAP2SeedIntervalSize: The maximum seeding interval size
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	85 --MAP2ZBest: Keep the z-best nodes during prefix trie traversal
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	86 --MAP2ReverseTrigger: The # seeds to trigger reverse alignment
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	88 --MAP3: Flag to run MAP3 in the second stage
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	89 --MAP3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	90 --MAP3SeedMaxHits: The maximum number of hits returned by a seed
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	91 --MAP3SeedWindow: The window of bases in which to group seeds
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	92 --MAP3HPEnumeration: The single homopolymer error difference for enumeration
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	93
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	94 --suppressHeader: Suppress header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	95 --dbkey: Dbkey for reference genome
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	96 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	97 """
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	98
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	99 import optparse, os, shutil, subprocess, sys, tempfile
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	100
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	101 def stop_err( msg ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	102 sys.stderr.write( '%s\n' % msg )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 sys.exit()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	104
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	105 def map1_parse( map1SeedLength, map1SeedMismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 map1SecondarySeedLength, map1NumEdits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	107 map1BaseError, map1Mismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	109 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	110 return '-l %s -s %s -L %s -p %s -P %s -m %s -o %s -e %s -d %s -i %s -b %s -Q %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	111 (map1SeedLength, map1SeedMismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	112 map1SecondarySeedLength, map1NumEdits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	113 map1BaseError, map1Mismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	117 def map2_parse( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	118 return '-c %s -S %s -b %s -N %s' % ( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	120 def map3_parse( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	121 return '-l %s -S %s -b %s -H %s' % ( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	122
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	123 def __main__():
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	124 #Parse Command Line
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125 parser = optparse.OptionParser()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 # Global options
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	127 parser.add_option( '--threads', dest='threads', help='The number of threads to use' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	128 parser.add_option( '--ref', dest='ref', help='The reference genome to use or index' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	129 parser.add_option( '--fastq', dest='fastq', help='The fastq file to use for the mapping' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	130 parser.add_option( '--output', dest='output', help='The file to save the output (SAM format)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	131 parser.add_option( '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	132 parser.add_option( '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	133 parser.add_option( '--mapall', dest='mapall', help='Flag indicating if mapall options are present')
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	134 parser.add_option( '--matchScore', dest='matchScore', help='The match score' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	135 parser.add_option( '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	136 parser.add_option( '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	137 parser.add_option( '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	138 parser.add_option( '--flowPenalty', dest='flowPenalty', help='Flow score penalty' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	139 parser.add_option( '--flowOrder', dest='flowOrder', help='Flow order' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	140 parser.add_option( '--bandWidth', dest='bandWidth', help='The band width' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	141 parser.add_option( '--globalMap', dest='globalMap', help='Map the full read (no soft-clipping)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	142 parser.add_option( '--duplicateWindow', dest='duplicateWindow', help='Remove duplicate alignments from different algorithms within this bp window (-1 to disable)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	143 parser.add_option( '--scoringThreshold', dest='scoringThreshold', help='The score threshold divided by the match score ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	144 parser.add_option( '--queueSize', dest='queueSize', help='The queue size for the reads' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	145 parser.add_option( '--outputFilter', dest='outputFilter', help='The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	146 parser.add_option( '--rgTag', dest='rgTag', help='The flag to specify RG tag(s) in the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	147 parser.add_option( '--rgTagID', dest='rgTagID', default='', help='The RG ID to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	148 parser.add_option( '--rgTagCN', dest='rgTagCN', default='', help='The RG CN to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	149 parser.add_option( '--rgTagDS', dest='rgTagDS', default='', help='The RG DS to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	150 parser.add_option( '--rgTagDT', dest='rgTagDT', default='', help='The RG DT to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	151 parser.add_option( '--rgTagLB', dest='rgTagLB', default='', help='The RG LB to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	152 parser.add_option( '--rgTagPI', dest='rgTagPI', default='', help='The RG PI to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	153 parser.add_option( '--rgTagPL', dest='rgTagPL', default='', help='The RG PL to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	154 parser.add_option( '--rgTagPU', dest='rgTagPU', default='', help='The RG PU to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	155 parser.add_option( '--rgTagSM', dest='rgTagSM', default='', help='The RG SM to add to the SAM header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	156 parser.add_option( '--filterIndependently', dest='filterIndependently', help='Apply the output filter for each algorithm independently' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	157 parser.add_option( '--suppressHeader', dest='suppressHeader', help='Suppress header' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	158 parser.add_option( '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	159 parser.add_option( '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	160 # map 1 - stage 1
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	161 parser.add_option( '--map1', dest='map1', help='True if map1 should be run in the first stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	162 parser.add_option( '--map1SeedLength', dest='map1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	163 parser.add_option( '--map1SeedMismatches', dest='map1SeedMismatches', help='The maximum number of mismatches in the seed ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	164 parser.add_option( '--map1SecondarySeedLength', dest='map1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	165 parser.add_option( '--map1NumEdits', dest='map1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	166 parser.add_option( '--map1BaseError', dest='map1BaseError', help='The assumed per-base maximum error rate' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	167 parser.add_option( '--map1Mismatches', dest='map1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	168 parser.add_option( '--map1GapOpens', dest='map1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	169 parser.add_option( '--map1GapExtensions', dest='map1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	170 parser.add_option( '--map1MaxCALsDeletion', dest='map1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	171 parser.add_option( '--map1EndIndels', dest='map1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	172 parser.add_option( '--map1MaxOptimalCALs', dest='map1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	173 parser.add_option( '--map1MaxNodes', dest='map1MaxNodes', help='The maximum number of alignment nodes ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	174 # map 2 - stage 1
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	175 parser.add_option( '--map2', dest='map2', help='True if map2 should be run in the first stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	176 parser.add_option( '--map2Coefficient', dest='map2Coefficient', help='The coefficient of length-threshold adjustment ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	177 parser.add_option( '--map2SeedIntervalSize', dest='map2SeedIntervalSize', help='The maximum seeding interval size ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	178 parser.add_option( '--map2ZBest', dest='map2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	179 parser.add_option( '--map2ReverseTrigger', dest='map2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	180 # map 3 - stage 1
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	181 parser.add_option( '--map3', dest='map3', help='True if map3 should be run in the first stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	182 parser.add_option( '--map3SeedLength', dest='map3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	183 parser.add_option( '--map3SeedMaxHits', dest='map3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	184 parser.add_option( '--map3SeedWindow', dest='map3SeedWindow', help='The window of bases in which to group seeds ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	185 parser.add_option( '--map3HPEnumeration', dest='map3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	186 # map 1 - stage 2
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	187 parser.add_option( '--MAP1', dest='MAP1', help='True if map1 should be run in the second stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	188 parser.add_option( '--MAP1SeedLength', dest='MAP1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	189 parser.add_option( '--MAP1SeedMismatches', dest='MAP1SeedMismatches', help='The maximum number of mismatches in the seed ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	190 parser.add_option( '--MAP1SecondarySeedLength', dest='MAP1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	191 parser.add_option( '--MAP1NumEdits', dest='MAP1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	192 parser.add_option( '--MAP1BaseError', dest='MAP1BaseError', help='The assumed per-base maximum error rate' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	193 parser.add_option( '--MAP1Mismatches', dest='MAP1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	194 parser.add_option( '--MAP1GapOpens', dest='MAP1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	195 parser.add_option( '--MAP1GapExtensions', dest='MAP1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	196 parser.add_option( '--MAP1MaxCALsDeletion', dest='MAP1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	197 parser.add_option( '--MAP1EndIndels', dest='MAP1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	198 parser.add_option( '--MAP1MaxOptimalCALs', dest='MAP1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	199 parser.add_option( '--MAP1MaxNodes', dest='MAP1MaxNodes', help='The maximum number of alignment nodes ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	200 # map 2 - stage 2
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	201 parser.add_option( '--MAP2', dest='MAP2', help='True if map2 should be run in the second stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	202 parser.add_option( '--MAP2Coefficient', dest='MAP2Coefficient', help='The coefficient of length-threshold adjustment ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	203 parser.add_option( '--MAP2SeedIntervalSize', dest='MAP2SeedIntervalSize', help='The maximum seeding interval size ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	204 parser.add_option( '--MAP2ZBest', dest='MAP2ZBest', help='Keep the z-best nodes during prefix trie traversal' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	205 parser.add_option( '--MAP2ReverseTrigger', dest='MAP2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	206 # map 3 - stage 2
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	207 parser.add_option( '--MAP3', dest='MAP3', help='True if map3 should be run in the second stage' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	208 parser.add_option( '--MAP3SeedLength', dest='MAP3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	209 parser.add_option( '--MAP3SeedMaxHits', dest='MAP3SeedMaxHits', help='The maximum number of hits returned by a seed ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	210 parser.add_option( '--MAP3SeedWindow', dest='MAP3SeedWindow', help='The window of bases in which to group seeds ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	211 parser.add_option( '--MAP3HPEnumeration', dest='MAP3HPEnumeration', help='The single homopolymer error difference for enumeration ' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	212 # parse the options
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	213 (options, args) = parser.parse_args()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	214
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	215 # output version # of tool
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	216 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	217 tmp = tempfile.NamedTemporaryFile().name
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	218 tmp_stdout = open( tmp, 'wb' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	219 proc = subprocess.Popen( args='tmap --version 2>&1', shell=True, stdout=tmp_stdout )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	220 tmp_stdout.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	221 returncode = proc.wait()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	222 stdout = None
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	223 for line in open( tmp_stdout.name, 'rb' ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	224 if line.lower().find( 'version' ) >= 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	225 stdout = line.strip()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	226 break
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	227 if stdout:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	228 sys.stdout.write( 'TMAP %s\n' % stdout )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	229 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	230 raise Exception
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	231 except:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	232 sys.stdout.write( 'Could not determine TMAP version\n' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	233
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	234 fastq = options.fastq
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	235
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	236 # make temp directory for placement of indices
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	237 tmp_index_dir = tempfile.mkdtemp()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	238 tmp_dir = tempfile.mkdtemp()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	239
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	240 # index if necessary
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	241 if options.fileSource == 'history' and not options.do_not_build_index:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	242 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	243 ref_file_name = ref_file.name
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	244 ref_file.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	245 os.symlink( options.ref, ref_file_name )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	246 cmd1 = 'tmap index -f %s -v ' % ( ref_file_name )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	247 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	248 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	249 tmp_stderr = open( tmp, 'wb' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	250 proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	251 returncode = proc.wait()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	252 tmp_stderr.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	253 # get stderr, allowing for case where it's very large
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	254 tmp_stderr = open( tmp, 'rb' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	255 stderr = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	256 buffsize = 1048576
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	257 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	258 while True:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	259 stderr += tmp_stderr.read( buffsize )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	260 if not stderr or len( stderr ) % buffsize != 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	261 break
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	262 except OverflowError:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	263 pass
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	264 tmp_stderr.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	265 if returncode != 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	266 raise Exception, stderr
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	267 except Exception, e:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	268 # clean up temp dirs
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	269 if os.path.exists( tmp_index_dir ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	270 shutil.rmtree( tmp_index_dir )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	271 if os.path.exists( tmp_dir ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	272 shutil.rmtree( tmp_dir )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	273 stop_err( 'Error indexing reference sequence. ' + str( e ) )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	274 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	275 ref_file_name = options.ref
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	276
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	277 # set up mapping and generate mapping command options
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	278 if options.params == 'pre_set':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	279 mapall_options = '-n %s' % ( options.threads )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	280 map1_options = 'map1'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	281 map2_options = 'map2'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	282 map3_options = 'map3'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	283 MAP1_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	284 MAP2_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	285 MAP3_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	286 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	287 # mapall options
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	288 if options.rgTag == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	289 rgTag = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	290 if options.rgTagID != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	291 rgTag += '-R "ID:' + options.rgTagID + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	292 if options.rgTagCN != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	293 rgTag += '-R "CN:' + options.rgTagCN + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	294 if options.rgTagDS != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	295 rgTag += '-R "DS:' + options.rgTagDS + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	296 if options.rgTagDT != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	297 rgTag += '-R "DT:' + options.rgTagDT + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	298 if options.rgTagLB != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	299 rgTag += '-R "LB:' + options.rgTagLB + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	300 if options.rgTagPI != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	301 rgTag += '-R "PI:' + options.rgTagPI + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	302 if options.rgTagPL != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	303 rgTag += '-R "PL:' + options.rgTagPL + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	304 if options.rgTagPU != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	305 rgTag += '-R "PU:' + options.rgTagPU + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	306 if options.rgTagSM != '':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	307 rgTag += '-R "SM:' + options.rgTagSM + '" '
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	308 rgTag.rstrip(' ')
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	309 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	310 rgTag = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	311 if None != options.flowOrder and '' != options.flowOrder:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	312 flowOrder = '-x ' + options.flowOrder
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	313 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	314 flowOrder = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	315 if options.filterIndependently == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	316 filterIndependently = '-I'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	317 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	318 filterIndependently = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	319 if options.mapall == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	320 mapall_options = '-A %s -M %s -O %s -E %s -X %s %s %s -W %s -T %s -q %s -n %s -a %s %s %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	321 ( options.matchScore, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	322 options.flowPenalty, flowOrder,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	323 options.globalMap, options.duplicateWindow, options.scoringThreshold, options.queueSize,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	324 options.threads, options.outputFilter, rgTag, filterIndependently )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	325 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	326 mapall_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	327
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	328 # map1 - stage one
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	329 if options.map1 == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	330 map1_options = 'map1 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	331 map1_parse( options.map1SeedLength, options.map1SeedMismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	332 options.map1SecondarySeedLength, options.map1NumEdits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	333 options.map1BaseError, options.map1Mismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	334 options.map1GapOpens, options.map1GapExtensions, options.map1MaxCALsDeletion, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	335 options.map1EndIndels, options.map1MaxOptimalCALs, options.map1MaxNodes )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	336 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	337 map1_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	338 # map2 - stage one
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	339 if options.map2 == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	340 map2_options = 'map2 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	341 map2_parse( options.map2Coefficient, options.map2SeedIntervalSize, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	342 options.map2ZBest, options.map2ReverseTrigger )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	343 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	344 map2_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	345 # map3 - stage one
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	346 if options.map3 == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	347 map3_options = 'map3 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	348 map3_parse( options.map3SeedLength, options.map3SeedMaxHits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	349 options.map3SeedWindow, options.map3HPEnumeration )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	350 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	351 map3_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	352 # map1 - stage two
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	353 if options.MAP1== 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	354 MAP1_options = 'MAP1 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	355 map1_parse( options.MAP1SeedLength, options.MAP1SeedMismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	356 options.MAP1SecondarySeedLength, options.MAP1NumEdits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	357 options.MAP1BaseError, options.MAP1Mismatches, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	358 options.MAP1GapOpens, options.MAP1GapExtensions, options.MAP1MaxCALsDeletion, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	359 options.MAP1EndIndels, options.MAP1MaxOptimalCALs, options.MAP1MaxNodes )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	360 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	361 MAP1_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	362 # map2 - stage two
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	363 if options.MAP2 == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	364 MAP2_options = 'MAP2 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	365 map2_parse( options.MAP2Coefficient, options.MAP2SeedIntervalSize, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	366 options.MAP2ZBest, options.MAP2ReverseTrigger )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	367 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	368 MAP2_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	369 # map3 - stage two
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	370 if options.MAP3 == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	371 MAP3_options = 'MAP3 %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	372 MAP3_parse( options.MAP3SeedLength, options.MAP3SeedMaxHits, \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	373 options.MAP3SeedWindow, options.MAP3HPEnumeration )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	374 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	375 MAP3_options = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	376
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	377 #mapping_cmds
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	378 # prepare actual mapping and generate mapping commands
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	379 cmd2 = 'tmap mapall -f %s -r %s -F fastq %s -v %s %s %s %s %s %s > %s' % \
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	380 ( ref_file_name, fastq, mapall_options,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	381 map1_options, map2_options, map3_options,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	382 MAP1_options, MAP2_options, MAP3_options,
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	383 options.output )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	384 # perform alignments
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	385 buffsize = 1048576
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	386 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	387 # need to nest try-except in try-finally to handle 2.4
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	388 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	389 # align
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	390 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	391 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	392 tmp_stderr = open( tmp, 'wb' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	393 proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	394 returncode = proc.wait()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	395 tmp_stderr.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	396 # get stderr, allowing for case where it's very large
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	397 tmp_stderr = open( tmp, 'rb' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	398 stderr = ''
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	399 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	400 while True:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	401 stderr += tmp_stderr.read( buffsize )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	402 if not stderr or len( stderr ) % buffsize != 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	403 break
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	404 except OverflowError:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	405 pass
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	406 tmp_stderr.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	407 if returncode != 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	408 raise Exception, stderr
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	409 except Exception, e:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	410 raise Exception, 'Error mapping sequence. ' + str( e )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	411 # remove header if necessary
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	412 if options.suppressHeader == 'true':
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	413 tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	414 tmp_out_name = tmp_out.name
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	415 tmp_out.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	416 try:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	417 shutil.move( options.output, tmp_out_name )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	418 except Exception, e:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	419 raise Exception, 'Error moving output file before removing headers. ' + str( e )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	420 fout = file( options.output, 'w' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	421 for line in file( tmp_out.name, 'r' ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	422 if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	423 fout.write( line )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	424 fout.close()
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	425 # check that there are results in the output file
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	426 if os.path.getsize( options.output ) > 0:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	427 sys.stdout.write( 'TMAP completed' )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	428 else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	429 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.'
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	430 except Exception, e:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	431 stop_err( 'The alignment failed.\n' + str( e ) )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	432 finally:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	433 # clean up temp dir
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	434 if os.path.exists( tmp_index_dir ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	435 shutil.rmtree( tmp_index_dir )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	436 if os.path.exists( tmp_dir ):
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	437 shutil.rmtree( tmp_dir )
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	438
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	439 if __name__=="__main__": __main__()

Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.0.19/tmap_wrapper.py @ 1:40ade4f81a30 default tip