tmap_wrapper: tmap_wrapper_0.0.19/tmap

author	nilshomer
date	Tue, 07 Jun 2011 16:46:26 -0400
parents
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.
de2efe4dda3f 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.
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
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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)
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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")
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	41
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	55
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	61
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	81
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	93
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	94 --suppressHeader: Suppress header
de2efe4dda3f 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
de2efe4dda3f 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'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	97 """
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	98
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	100
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 sys.exit()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	104
de2efe4dda3f 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, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 map1SecondarySeedLength, map1NumEdits, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	107 map1BaseError, map1Mismatches, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	109 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes ):
de2efe4dda3f 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' % \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	111 (map1SeedLength, map1SeedMismatches, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	112 map1SecondarySeedLength, map1NumEdits, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	113 map1BaseError, map1Mismatches, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	122
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	123 def __main__():
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	124 #Parse Command Line
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125 parser = optparse.OptionParser()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 # Global options
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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)' )
de2efe4dda3f 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)' )
de2efe4dda3f 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)' )
de2efe4dda3f 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')
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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)' )
de2efe4dda3f 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)' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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' )
de2efe4dda3f 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)' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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" )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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)' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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)' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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) ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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)' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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)' )
de2efe4dda3f 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' )
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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) ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f 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 ' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	212 # parse the options
de2efe4dda3f 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()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	214
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	216 try:
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	220 tmp_stdout.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	221 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	222 stdout = None
de2efe4dda3f 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' ):
de2efe4dda3f 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:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	225 stdout = line.strip()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	226 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	227 if stdout:
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	229 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	230 raise Exception
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	231 except:
de2efe4dda3f 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' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	233
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	234 fastq = options.fastq
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	235
de2efe4dda3f 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
de2efe4dda3f 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()
de2efe4dda3f 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()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	239
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	240 # index if necessary
de2efe4dda3f 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:
de2efe4dda3f 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 )
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	244 ref_file.close()
de2efe4dda3f 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 )
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	247 try:
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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() )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	251 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	252 tmp_stderr.close()
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	255 stderr = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	256 buffsize = 1048576
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	257 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	258 while True:
de2efe4dda3f 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 )
de2efe4dda3f 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:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	261 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	262 except OverflowError:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	263 pass
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	264 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	265 if returncode != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	266 raise Exception, stderr
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	267 except Exception, e:
de2efe4dda3f 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
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
de2efe4dda3f 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 ) )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	274 else:
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	276
de2efe4dda3f 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
de2efe4dda3f 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':
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	280 map1_options = 'map1'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	281 map2_options = 'map2'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	282 map3_options = 'map3'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	283 MAP1_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	284 MAP2_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	285 MAP3_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	286 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	287 # mapall options
de2efe4dda3f 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':
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	289 rgTag = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	290 if options.rgTagID != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	292 if options.rgTagCN != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	294 if options.rgTagDS != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	296 if options.rgTagDT != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	298 if options.rgTagLB != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	300 if options.rgTagPI != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	302 if options.rgTagPL != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	304 if options.rgTagPU != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	306 if options.rgTagSM != '':
de2efe4dda3f 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 + '" '
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	308 rgTag.rstrip(' ')
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	309 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	310 rgTag = ''
de2efe4dda3f 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:
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	313 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	314 flowOrder = ''
de2efe4dda3f 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':
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	316 filterIndependently = '-I'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	317 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	318 filterIndependently = ''
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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,
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	322 options.flowPenalty, flowOrder,
de2efe4dda3f 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,
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	325 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	326 mapall_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	327
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	328 # map1 - stage one
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	336 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	337 map1_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	338 # map2 - stage one
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	343 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	344 map2_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	345 # map3 - stage one
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	350 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	351 map3_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	352 # map1 - stage two
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	360 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	361 MAP1_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	362 # map2 - stage two
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	367 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	368 MAP2_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	369 # map3 - stage two
de2efe4dda3f 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':
de2efe4dda3f 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' % \
de2efe4dda3f 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, \
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	374 else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	375 MAP3_options = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	376
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	377 #mapping_cmds
de2efe4dda3f 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
de2efe4dda3f 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' % \
de2efe4dda3f 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,
de2efe4dda3f 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,
de2efe4dda3f 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,
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	383 options.output )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	384 # perform alignments
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	385 buffsize = 1048576
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	386 try:
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	388 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	389 # align
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	390 try:
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f 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() )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	394 returncode = proc.wait()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	395 tmp_stderr.close()
de2efe4dda3f 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
de2efe4dda3f 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' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	398 stderr = ''
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	399 try:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	400 while True:
de2efe4dda3f 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 )
de2efe4dda3f 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:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	403 break
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	404 except OverflowError:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	405 pass
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	406 tmp_stderr.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	407 if returncode != 0:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	408 raise Exception, stderr
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	409 except Exception, e:
de2efe4dda3f 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 )
de2efe4dda3f 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
de2efe4dda3f 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':
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	415 tmp_out.close()
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	416 try:
de2efe4dda3f 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 )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	418 except Exception, e:
de2efe4dda3f 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 )
de2efe4dda3f 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' )
de2efe4dda3f 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' ):
de2efe4dda3f 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' ) ):
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	423 fout.write( line )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	424 fout.close()
de2efe4dda3f 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
de2efe4dda3f 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:
de2efe4dda3f 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' )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	428 else:
de2efe4dda3f 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.'
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	430 except Exception, e:
de2efe4dda3f 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 ) )
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	432 finally:
de2efe4dda3f 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
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de2efe4dda3f 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 )
de2efe4dda3f 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 ):
de2efe4dda3f 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 )
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0

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1 #!/usr/bin/env python

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2

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3 # TODO

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4 # - map1/map2/map3 specific options

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5

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6 """

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7 Runs TMAP on Ion Torrent data.

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8 Produces a SAM file containing the mappings.

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9 Works with TMAP version 0.0.19 or higher.

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10

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11 usage: tmap_wrapper.py [options]

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12 --threads: The number of threads to use

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13 --ref: The reference genome to use or index

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14 --fastq: The fastq file to use for the mapping

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15 --output: The file to save the output (SAM format)

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16 --params: Parameter setting to use (pre_set or full)

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17 --fileSource: Whether to use a previously indexed reference sequence or one from history (indexed or history)

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18 --matchScore: The match score

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19 --mismatchPenalty: The ismatch penalty

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20 --gapOpenPenalty: The gap open penalty

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21 --gapExtensPenalty: The gap extension penalty

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22 --flowPenalty: The flow score penalty

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23 --flowOrder: The flow order ([ACGT]{4+} or "sff")

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24 --bandWidth: The band width

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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)

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26 --duplicateWindow: Remove duplicate alignments from different algorithms within this bp window (-1 to disable)

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27 --scoringThreshold: The score threshold divided by the match score

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28 --queueSize: The queue size for the reads

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29 --outputFilter: The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)

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30 --rgTag: The flag to specify RG tag(s) in the SAM header

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31 --rgTagID: The RG ID tag to add to the SAM header

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32 --rgTagCN: The RG CN tag to add to the SAM header

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33 --rgTagDS: The RG DS tag to add to the SAM header

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34 --rgTagDT: The RG DT tag to add to the SAM header

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35 --rgTagLB: The RG LB tag to add to the SAM header

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36 --rgTagPI: The RG PI tag to add to the SAM header

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37 --rgTagPL: The RG PL tag to add to the SAM header

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38 --rgTagPU: The RG PU tag to add to the SAM header

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39 --rgTagSM: The RG SM tag to add to the SAM header

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40 --filterIndependently: Apply the output filter for each algorithm independently

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41

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42 --map1: Flag to run map1 in the first stage

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43 --map1SeedLength: The k-mer length to seed CALs (-1 to disable)

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44 --map1SeedMismatches: The maximum number of mismatches in the seed

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45 --map1SecondarySeedLength: The secondary seed length (-1 to disable)

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46 --map1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate

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47 --map1BaseError: The assumed per-base maximum error rate

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48 --map1Mismatches: The maximum number of or (read length) fraction of mismatches

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49 --map1GapOpens: The maximum number of or (read length) fraction of indel starts

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50 --map1GapExtensions: The maximum number of or (read length) fraction of indel extensions

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51 --map1MaxCALsDeletion: The maximum number of CALs to extend a deletion

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52 --map1EndIndels: Indels are not allowed within this number of bps from the end of the read

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53 --map1MaxOptimalCALs: Stop searching when INT optimal CALs have been found

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54 --map1MaxNodes: The maximum number of alignment nodes

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55

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56 --map2: Flag to run map2 in the first stage

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57 --map2Coefficient: The coefficient of length-threshold adjustment

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58 --map2SeedIntervalSize: The maximum seeding interval size

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59 --map2ZBest: Keep the z-best nodes during prefix trie traversal

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60 --map2ReverseTrigger: The # seeds to trigger reverse alignment

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61

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62 --map3: Flag to run map3 in the first stage

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63 --map3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)

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64 --map3SeedMaxHits: The maximum number of hits returned by a seed

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65 --map3SeedWindow: The window of bases in which to group seeds

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66 --map3HPEnumeration: The single homopolymer error difference for enumeration

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67

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68 --MAP1: Flag to run MAP1 in the second stage

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69 --MAP1SeedLength: The k-mer length to seed CALs (-1 to disable)

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70 --MAP1SeedMismatches: The maximum number of mismatches in the seed

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71 --MAP1SecondarySeedLength: The secondary seed length (-1 to disable)

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72 --MAP1NumEdits: The maximum number of edits or false-negative probability assuming the maximum error rate

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73 --MAP1BaseError: The assumed per-base maximum error rate

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74 --MAP1Mismatches: The maximum number of or (read length) fraction of mismatches

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75 --MAP1GapOpens: The maximum number of or (read length) fraction of indel starts

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76 --MAP1GapExtensions: The maximum number of or (read length) fraction of indel extensions

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77 --MAP1MaxCALsDeletion: The maximum number of CALs to extend a deletion

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78 --MAP1EndIndels: Indels are not allowed within this number of bps from the end of the read

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79 --MAP1MaxOptimalCALs: Stop searching when INT optimal CALs have been found

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80 --MAP1MaxNodes: The maximum number of alignment nodes

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81

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82 --MAP2: Flag to run MAP2 in the second stage

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83 --MAP2Coefficient: The coefficient of length-threshold adjustment

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84 --MAP2SeedIntervalSize: The maximum seeding interval size

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85 --MAP2ZBest: Keep the z-best nodes during prefix trie traversal

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86 --MAP2ReverseTrigger: The # seeds to trigger reverse alignment

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87

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88 --MAP3: Flag to run MAP3 in the second stage

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89 --MAP3SeedLength: The k-mer length to seed CALs (-1 tunes to the genome size)

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90 --MAP3SeedMaxHits: The maximum number of hits returned by a seed

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91 --MAP3SeedWindow: The window of bases in which to group seeds

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92 --MAP3HPEnumeration: The single homopolymer error difference for enumeration

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93

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94 --suppressHeader: Suppress header

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95 --dbkey: Dbkey for reference genome

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96 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'

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97 """

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98

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99 import optparse, os, shutil, subprocess, sys, tempfile

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100

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101 def stop_err( msg ):

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102 sys.stderr.write( '%s\n' % msg )

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103 sys.exit()

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104

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105 def map1_parse( map1SeedLength, map1SeedMismatches, \

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106 map1SecondarySeedLength, map1NumEdits, \

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107 map1BaseError, map1Mismatches, \

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108 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \

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109 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes ):

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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' % \

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111 (map1SeedLength, map1SeedMismatches, \

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112 map1SecondarySeedLength, map1NumEdits, \

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113 map1BaseError, map1Mismatches, \

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114 map1GapOpens, map1GapExtensions, map1MaxCALsDeletion, \

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115 map1EndIndels, map1MaxOptimalCALs, map1MaxNodes )

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116

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117 def map2_parse( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger ):

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118 return '-c %s -S %s -b %s -N %s' % ( map2Coefficient, map2SeedIntervalSize, map2ZBest, map2ReverseTrigger )

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119

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120 def map3_parse( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration ):

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121 return '-l %s -S %s -b %s -H %s' % ( map3SeedLength, map3SeedMaxHits, map3SeedWindow, map3HPEnumeration )

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122

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123 def __main__():

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124 #Parse Command Line

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125 parser = optparse.OptionParser()

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126 # Global options

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127 parser.add_option( '--threads', dest='threads', help='The number of threads to use' )

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128 parser.add_option( '--ref', dest='ref', help='The reference genome to use or index' )

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diff changeset

129 parser.add_option( '--fastq', dest='fastq', help='The fastq file to use for the mapping' )

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130 parser.add_option( '--output', dest='output', help='The file to save the output (SAM format)' )

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diff changeset

131 parser.add_option( '--params', dest='params', help='Parameter setting to use (pre_set or full)' )

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132 parser.add_option( '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one from history (indexed or history)' )

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133 parser.add_option( '--mapall', dest='mapall', help='Flag indicating if mapall options are present')

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134 parser.add_option( '--matchScore', dest='matchScore', help='The match score' )

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135 parser.add_option( '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )

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136 parser.add_option( '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )

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137 parser.add_option( '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )

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138 parser.add_option( '--flowPenalty', dest='flowPenalty', help='Flow score penalty' )

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139 parser.add_option( '--flowOrder', dest='flowOrder', help='Flow order' )

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140 parser.add_option( '--bandWidth', dest='bandWidth', help='The band width' )

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141 parser.add_option( '--globalMap', dest='globalMap', help='Map the full read (no soft-clipping)' )

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142 parser.add_option( '--duplicateWindow', dest='duplicateWindow', help='Remove duplicate alignments from different algorithms within this bp window (-1 to disable)' )

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143 parser.add_option( '--scoringThreshold', dest='scoringThreshold', help='The score threshold divided by the match score ' )

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144 parser.add_option( '--queueSize', dest='queueSize', help='The queue size for the reads' )

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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)' )

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146 parser.add_option( '--rgTag', dest='rgTag', help='The flag to specify RG tag(s) in the SAM header' )

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147 parser.add_option( '--rgTagID', dest='rgTagID', default='', help='The RG ID to add to the SAM header' )

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148 parser.add_option( '--rgTagCN', dest='rgTagCN', default='', help='The RG CN to add to the SAM header' )

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149 parser.add_option( '--rgTagDS', dest='rgTagDS', default='', help='The RG DS to add to the SAM header' )

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150 parser.add_option( '--rgTagDT', dest='rgTagDT', default='', help='The RG DT to add to the SAM header' )

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151 parser.add_option( '--rgTagLB', dest='rgTagLB', default='', help='The RG LB to add to the SAM header' )

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152 parser.add_option( '--rgTagPI', dest='rgTagPI', default='', help='The RG PI to add to the SAM header' )

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153 parser.add_option( '--rgTagPL', dest='rgTagPL', default='', help='The RG PL to add to the SAM header' )

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154 parser.add_option( '--rgTagPU', dest='rgTagPU', default='', help='The RG PU to add to the SAM header' )

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155 parser.add_option( '--rgTagSM', dest='rgTagSM', default='', help='The RG SM to add to the SAM header' )

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156 parser.add_option( '--filterIndependently', dest='filterIndependently', help='Apply the output filter for each algorithm independently' )

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157 parser.add_option( '--suppressHeader', dest='suppressHeader', help='Suppress header' )

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158 parser.add_option( '--dbkey', dest='dbkey', help='Dbkey for reference genome' )

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159 parser.add_option( '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )

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160 # map 1 - stage 1

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161 parser.add_option( '--map1', dest='map1', help='True if map1 should be run in the first stage' )

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162 parser.add_option( '--map1SeedLength', dest='map1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )

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163 parser.add_option( '--map1SeedMismatches', dest='map1SeedMismatches', help='The maximum number of mismatches in the seed ' )

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164 parser.add_option( '--map1SecondarySeedLength', dest='map1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )

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165 parser.add_option( '--map1NumEdits', dest='map1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )

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166 parser.add_option( '--map1BaseError', dest='map1BaseError', help='The assumed per-base maximum error rate' )

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167 parser.add_option( '--map1Mismatches', dest='map1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )

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168 parser.add_option( '--map1GapOpens', dest='map1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )

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169 parser.add_option( '--map1GapExtensions', dest='map1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )

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170 parser.add_option( '--map1MaxCALsDeletion', dest='map1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )

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171 parser.add_option( '--map1EndIndels', dest='map1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )

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172 parser.add_option( '--map1MaxOptimalCALs', dest='map1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )

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173 parser.add_option( '--map1MaxNodes', dest='map1MaxNodes', help='The maximum number of alignment nodes ' )

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174 # map 2 - stage 1

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175 parser.add_option( '--map2', dest='map2', help='True if map2 should be run in the first stage' )

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176 parser.add_option( '--map2Coefficient', dest='map2Coefficient', help='The coefficient of length-threshold adjustment ' )

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177 parser.add_option( '--map2SeedIntervalSize', dest='map2SeedIntervalSize', help='The maximum seeding interval size ' )

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178 parser.add_option( '--map2ZBest', dest='map2ZBest', help='Keep the z-best nodes during prefix trie traversal' )

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179 parser.add_option( '--map2ReverseTrigger', dest='map2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )

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180 # map 3 - stage 1

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181 parser.add_option( '--map3', dest='map3', help='True if map3 should be run in the first stage' )

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182 parser.add_option( '--map3SeedLength', dest='map3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )

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183 parser.add_option( '--map3SeedMaxHits', dest='map3SeedMaxHits', help='The maximum number of hits returned by a seed ' )

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184 parser.add_option( '--map3SeedWindow', dest='map3SeedWindow', help='The window of bases in which to group seeds ' )

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185 parser.add_option( '--map3HPEnumeration', dest='map3HPEnumeration', help='The single homopolymer error difference for enumeration ' )

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186 # map 1 - stage 2

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187 parser.add_option( '--MAP1', dest='MAP1', help='True if map1 should be run in the second stage' )

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188 parser.add_option( '--MAP1SeedLength', dest='MAP1SeedLength', help='The k-mer length to seed CALs (-1 to disable)' )

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189 parser.add_option( '--MAP1SeedMismatches', dest='MAP1SeedMismatches', help='The maximum number of mismatches in the seed ' )

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190 parser.add_option( '--MAP1SecondarySeedLength', dest='MAP1SecondarySeedLength', help='The secondary seed length (-1 to disable)' )

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191 parser.add_option( '--MAP1NumEdits', dest='MAP1NumEdits', help='The maximum number of edits or false-negative probability assuming the maximum error rate' )

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192 parser.add_option( '--MAP1BaseError', dest='MAP1BaseError', help='The assumed per-base maximum error rate' )

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193 parser.add_option( '--MAP1Mismatches', dest='MAP1Mismatches', help='The maximum number of or (read length) fraction of mismatches ' )

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194 parser.add_option( '--MAP1GapOpens', dest='MAP1GapOpens', help='The maximum number of or (read length) fraction of indel starts ' )

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195 parser.add_option( '--MAP1GapExtensions', dest='MAP1GapExtensions', help='The maximum number of or (read length) fraction of indel extensions ' )

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196 parser.add_option( '--MAP1MaxCALsDeletion', dest='MAP1MaxCALsDeletion', help='The maximum number of CALs to extend a deletion ' )

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197 parser.add_option( '--MAP1EndIndels', dest='MAP1EndIndels', help='Indels are not allowed within this number of bps from the end of the read ' )

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198 parser.add_option( '--MAP1MaxOptimalCALs', dest='MAP1MaxOptimalCALs', help='Stop searching when INT optimal CALs have been found ' )

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199 parser.add_option( '--MAP1MaxNodes', dest='MAP1MaxNodes', help='The maximum number of alignment nodes ' )

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200 # map 2 - stage 2

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201 parser.add_option( '--MAP2', dest='MAP2', help='True if map2 should be run in the second stage' )

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202 parser.add_option( '--MAP2Coefficient', dest='MAP2Coefficient', help='The coefficient of length-threshold adjustment ' )

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203 parser.add_option( '--MAP2SeedIntervalSize', dest='MAP2SeedIntervalSize', help='The maximum seeding interval size ' )

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204 parser.add_option( '--MAP2ZBest', dest='MAP2ZBest', help='Keep the z-best nodes during prefix trie traversal' )

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205 parser.add_option( '--MAP2ReverseTrigger', dest='MAP2ReverseTrigger', help='The # seeds to trigger reverse alignment ' )

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206 # map 3 - stage 2

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207 parser.add_option( '--MAP3', dest='MAP3', help='True if map3 should be run in the second stage' )

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208 parser.add_option( '--MAP3SeedLength', dest='MAP3SeedLength', help='The k-mer length to seed CALs (-1 tunes to the genome size) ' )

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209 parser.add_option( '--MAP3SeedMaxHits', dest='MAP3SeedMaxHits', help='The maximum number of hits returned by a seed ' )

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210 parser.add_option( '--MAP3SeedWindow', dest='MAP3SeedWindow', help='The window of bases in which to group seeds ' )

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211 parser.add_option( '--MAP3HPEnumeration', dest='MAP3HPEnumeration', help='The single homopolymer error difference for enumeration ' )

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212 # parse the options

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213 (options, args) = parser.parse_args()

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214

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215 # output version # of tool

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216 try:

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217 tmp = tempfile.NamedTemporaryFile().name

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218 tmp_stdout = open( tmp, 'wb' )

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219 proc = subprocess.Popen( args='tmap --version 2>&1', shell=True, stdout=tmp_stdout )

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220 tmp_stdout.close()

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221 returncode = proc.wait()

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222 stdout = None

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223 for line in open( tmp_stdout.name, 'rb' ):

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224 if line.lower().find( 'version' ) >= 0:

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225 stdout = line.strip()

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226 break

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227 if stdout:

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228 sys.stdout.write( 'TMAP %s\n' % stdout )

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229 else:

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230 raise Exception

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231 except:

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232 sys.stdout.write( 'Could not determine TMAP version\n' )

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233

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234 fastq = options.fastq

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235

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236 # make temp directory for placement of indices

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237 tmp_index_dir = tempfile.mkdtemp()

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diff changeset

238 tmp_dir = tempfile.mkdtemp()

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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239

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

240 # index if necessary

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nilshomer

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diff changeset

241 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

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diff changeset

242 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )

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nilshomer

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diff changeset

243 ref_file_name = ref_file.name

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

244 ref_file.close()

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

245 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

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diff changeset

246 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

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diff changeset

247 try:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

248 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

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diff changeset

249 tmp_stderr = open( tmp, 'wb' )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

250 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

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diff changeset

251 returncode = proc.wait()

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

252 tmp_stderr.close()

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

253 # 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

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254 tmp_stderr = open( tmp, 'rb' )

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nilshomer

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diff changeset

255 stderr = ''

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nilshomer

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diff changeset

256 buffsize = 1048576

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nilshomer

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diff changeset

257 try:

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nilshomer

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diff changeset

258 while True:

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nilshomer

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diff changeset

259 stderr += tmp_stderr.read( buffsize )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

260 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

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diff changeset

261 break

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

262 except OverflowError:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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263 pass

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

264 tmp_stderr.close()

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

265 if returncode != 0:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

266 raise Exception, stderr

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

267 except Exception, e:

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nilshomer

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diff changeset

268 # clean up temp dirs

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nilshomer

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diff changeset

269 if os.path.exists( tmp_index_dir ):

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diff changeset

270 shutil.rmtree( tmp_index_dir )

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nilshomer

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diff changeset

271 if os.path.exists( tmp_dir ):

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nilshomer

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diff changeset

272 shutil.rmtree( tmp_dir )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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273 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

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diff changeset

274 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

275 ref_file_name = options.ref

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276

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

277 # 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

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diff changeset

278 if options.params == 'pre_set':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

279 mapall_options = '-n %s' % ( options.threads )

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diff changeset

280 map1_options = 'map1'

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

281 map2_options = 'map2'

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

282 map3_options = 'map3'

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

283 MAP1_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

284 MAP2_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

285 MAP3_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

286 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

287 # mapall options

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

288 if options.rgTag == 'true':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

289 rgTag = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

290 if options.rgTagID != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

291 rgTag += '-R "ID:' + options.rgTagID + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

292 if options.rgTagCN != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

293 rgTag += '-R "CN:' + options.rgTagCN + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

294 if options.rgTagDS != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

295 rgTag += '-R "DS:' + options.rgTagDS + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

296 if options.rgTagDT != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

297 rgTag += '-R "DT:' + options.rgTagDT + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

298 if options.rgTagLB != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

299 rgTag += '-R "LB:' + options.rgTagLB + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

300 if options.rgTagPI != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

301 rgTag += '-R "PI:' + options.rgTagPI + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

302 if options.rgTagPL != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

303 rgTag += '-R "PL:' + options.rgTagPL + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

304 if options.rgTagPU != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

305 rgTag += '-R "PU:' + options.rgTagPU + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

306 if options.rgTagSM != '':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

307 rgTag += '-R "SM:' + options.rgTagSM + '" '

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

308 rgTag.rstrip(' ')

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

309 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

310 rgTag = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

311 if None != options.flowOrder and '' != options.flowOrder:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

312 flowOrder = '-x ' + options.flowOrder

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

313 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

314 flowOrder = ''

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

316 filterIndependently = '-I'

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

317 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

318 filterIndependently = ''

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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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' % \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

321 ( options.matchScore, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

322 options.flowPenalty, flowOrder,

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

323 options.globalMap, options.duplicateWindow, options.scoringThreshold, options.queueSize,

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

324 options.threads, options.outputFilter, rgTag, filterIndependently )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

325 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

326 mapall_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

327

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

328 # map1 - stage one

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

330 map1_options = 'map1 %s' % \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

331 map1_parse( options.map1SeedLength, options.map1SeedMismatches, \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

332 options.map1SecondarySeedLength, options.map1NumEdits, \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

333 options.map1BaseError, options.map1Mismatches, \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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parents:

diff changeset

334 options.map1GapOpens, options.map1GapExtensions, options.map1MaxCALsDeletion, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

336 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

337 map1_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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parents:

diff changeset

338 # map2 - stage one

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

340 map2_options = 'map2 %s' % \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

341 map2_parse( options.map2Coefficient, options.map2SeedIntervalSize, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

343 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

344 map2_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

345 # map3 - stage one

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

347 map3_options = 'map3 %s' % \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

348 map3_parse( options.map3SeedLength, options.map3SeedMaxHits, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

350 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

351 map3_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

352 # map1 - stage two

de2efe4dda3f 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':

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

354 MAP1_options = 'MAP1 %s' % \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

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diff changeset

355 map1_parse( options.MAP1SeedLength, options.MAP1SeedMismatches, \

de2efe4dda3f 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, \

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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diff changeset

357 options.MAP1BaseError, options.MAP1Mismatches, \

de2efe4dda3f 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, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

360 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

361 MAP1_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

362 # map2 - stage two

de2efe4dda3f 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':

de2efe4dda3f 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' % \

de2efe4dda3f 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, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

367 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

368 MAP2_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

369 # map3 - stage two

de2efe4dda3f 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':

de2efe4dda3f 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' % \

de2efe4dda3f 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, \

de2efe4dda3f 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 )

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

374 else:

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

375 MAP3_options = ''

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

376

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

parents:

diff changeset

377 #mapping_cmds

de2efe4dda3f 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

de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

nilshomer

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379 cmd2 = 'tmap mapall -f %s -r %s -F fastq %s -v %s %s %s %s %s %s > %s' % \

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380 ( ref_file_name, fastq, mapall_options,

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381 map1_options, map2_options, map3_options,

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382 MAP1_options, MAP2_options, MAP3_options,

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383 options.output )

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384 # perform alignments

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385 buffsize = 1048576

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386 try:

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387 # need to nest try-except in try-finally to handle 2.4

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388 try:

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389 # align

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390 try:

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391 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name

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392 tmp_stderr = open( tmp, 'wb' )

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393 proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )

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394 returncode = proc.wait()

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395 tmp_stderr.close()

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396 # get stderr, allowing for case where it's very large

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397 tmp_stderr = open( tmp, 'rb' )

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398 stderr = ''

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399 try:

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400 while True:

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401 stderr += tmp_stderr.read( buffsize )

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402 if not stderr or len( stderr ) % buffsize != 0:

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403 break

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404 except OverflowError:

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405 pass

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406 tmp_stderr.close()

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407 if returncode != 0:

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408 raise Exception, stderr

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409 except Exception, e:

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410 raise Exception, 'Error mapping sequence. ' + str( e )

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411 # remove header if necessary

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412 if options.suppressHeader == 'true':

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413 tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)

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414 tmp_out_name = tmp_out.name

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415 tmp_out.close()

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416 try:

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417 shutil.move( options.output, tmp_out_name )

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418 except Exception, e:

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419 raise Exception, 'Error moving output file before removing headers. ' + str( e )

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420 fout = file( options.output, 'w' )

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421 for line in file( tmp_out.name, 'r' ):

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422 if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):

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423 fout.write( line )

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424 fout.close()

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425 # check that there are results in the output file

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426 if os.path.getsize( options.output ) > 0:

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427 sys.stdout.write( 'TMAP completed' )

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428 else:

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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.'

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430 except Exception, e:

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431 stop_err( 'The alignment failed.\n' + str( e ) )

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432 finally:

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433 # clean up temp dir

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434 if os.path.exists( tmp_index_dir ):

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435 shutil.rmtree( tmp_index_dir )

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436 if os.path.exists( tmp_dir ):

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437 shutil.rmtree( tmp_dir )

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438

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439 if __name__=="__main__": __main__()

Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.0.19/tmap_wrapper.py @ 0:de2efe4dda3f