bowtie_color_wrappers: bowtie_wrapper.py annotate

annotate bowtie_wrapper.py @ 0:60661549b3e3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

author	devteam
date	Mon, 09 Nov 2015 11:17:57 -0500
parents
children

rev	line source
0 60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	1 #!/usr/bin/env python
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	2
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	3 """
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	4 Runs Bowtie on single-end or paired-end data.
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	5 For use with Bowtie v. 0.12.7
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	6
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	7 usage: bowtie_wrapper.py [options]
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	8 -t, --threads=t: The number of threads to run
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	9 -o, --output=o: The output file
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	10 --output_unmapped_reads=: File name for unmapped reads (single-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	11 --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	12 --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	13 --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	14 --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	15 --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	16 -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	17 -I, --input2=I: The reverse reads file in Sanger FASTQ format
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	18 -4, --dataType=4: The type of data (SOLiD or Solexa)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	19 -2, --paired=2: Whether the data is single- or paired-end
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	20 -g, --genomeSource=g: The type of reference provided
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	21 -r, --ref=r: The reference genome to use or index
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	22 -s, --skip=s: Skip the first n reads
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	23 -a, --alignLimit=a: Only align the first n reads
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	24 -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	25 -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	26 -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	27 -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	28 -l, --seedLen=l: Seed length
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	29 -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	30 -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	31 -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	32 -v, --valAlign=v: Report up to n valid arguments per read
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	33 -V, --allValAligns=V: Whether or not to report all valid alignments per read
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	34 -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	35 -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	36 -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	37 -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	38 -j, --minInsert=j: Minimum insert size for valid paired-end alignments
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	39 -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	40 -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	41 -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	42 -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	43 -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	44 -F, --offrate=F: Override the offrate of the index to n
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	45 -8, --snpphred=8: SNP penalty on Phred scale
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	46 -6, --snpfrac=6: Fraction of sites expected to be SNP sites
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	47 -7, --keepends=7: Keep extreme-end nucleotides and qualities
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	48 -S, --seed=S: Seed for pseudo-random number generator
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	49 -C, --params=C: Whether to use default or specified parameters
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	50 -u, --iautoB=u: Automatic or specified behavior
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	51 -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	52 -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	53 -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	54 -D, --idcv=D: The period for the difference-cover sample
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	55 -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	56 -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	57 -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	58 -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	59 -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	60 -N, --iendian=N: Endianness to use when serializing integers to the index file
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	61 -Z, --iseed=Z: Seed for the pseudorandom number generator
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	62 -c, --icutoff=c: Number of first bases of the reference sequence to index
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	63 -x, --indexSettings=x: Whether or not indexing options are to be set
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	64 -H, --suppressHeader=H: Suppress header
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	65 --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	66 """
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	67
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	68 import optparse, os, shutil, subprocess, sys, tempfile
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	69
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 #Allow more than Sanger encoded variants
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	71 DEFAULT_ASCII_ENCODING = '--phred33-quals'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	72 GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' }
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	73 #FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	74
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	75 def stop_err( msg ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	76 sys.stderr.write( '%s\n' % msg )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	77 sys.exit()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	78
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	79 def __main__():
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	80 #Parse Command Line
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 parser = optparse.OptionParser()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	82 parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	83 parser.add_option( '-o', '--output', dest='output', help='The output file' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	84 parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	85 parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	86 parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	87 parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	88 parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	89 parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	90 parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	91 parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	92 parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	93 parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	94 parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	96 parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	97 parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	100 parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	101 parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	102 parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	103 parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	104 parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	105 parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	106 parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	107 parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	108 parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	109 parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	110 parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	111 parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	112 parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	113 parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	114 parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	115 parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	116 parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	117 parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	121 parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	122 parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	123 parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	124 parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	125 parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	126 parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	127 parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	128 parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	129 parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	130 parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	131 parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	132 parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	133 parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	135 parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	136 parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	137 parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	138 parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	139 parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	140 parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	141 (options, args) = parser.parse_args()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	142 stdout = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	143
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	144 # make temp directory for placement of indices and copy reference file there if necessary
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 tmp_index_dir = tempfile.mkdtemp()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146 # get type of data (solid or solexa)
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	147 if options.dataType == 'solid':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	148 colorspace = '-C'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	149 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	150 colorspace = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	151 # index if necessary
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	152 if options.genomeSource == 'history' and not options.do_not_build_index:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	153 # set up commands
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	154 if options.index_settings =='indexPreSet':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	155 indexing_cmds = '%s' % colorspace
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	156 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	157 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	158 if options.iautoB and options.iautoB == 'set':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	159 iautoB = '--noauto'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	161 iautoB = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	162 if options. ipacked and options.ipacked == 'packed':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	163 ipacked = '--packed'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	164 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	165 ipacked = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166 if options.ibmax and int( options.ibmax ) >= 1:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	167 ibmax = '--bmax %s' % options.ibmax
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	168 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	169 ibmax = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	170 if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	171 ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	172 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 ibmaxdivn = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174 if options.idcv and int( options.idcv ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	175 idcv = '--dcv %s' % options.idcv
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	176 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	177 idcv = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	178 if options.inodc and options.inodc == 'nodc':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	179 inodc = '--nodc'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	180 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	181 inodc = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	182 if options.inoref and options.inoref == 'noref':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	183 inoref = '--noref'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	184 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 inoref = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	186 if options.iftab and int( options.iftab ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	187 iftab = '--ftabchars %s' % options.iftab
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	188 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 iftab = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 if options.intoa and options.intoa == 'yes':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	191 intoa = '--ntoa'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	192 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	193 intoa = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	194 if options.iendian and options.iendian == 'big':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	195 iendian = '--big'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	196 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	197 iendian = '--little'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 if options.iseed and int( options.iseed ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	199 iseed = '--seed %s' % options.iseed
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	200 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 iseed = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	202 if options.icutoff and int( options.icutoff ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	203 icutoff = '--cutoff %s' % options.icutoff
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	205 icutoff = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	206 indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207 ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	208 inoref, options.ioffrate, iftab, intoa, iendian,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	209 iseed, icutoff, colorspace )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	210 except ValueError, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	211 # clean up temp dir
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 if os.path.exists( tmp_index_dir ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213 shutil.rmtree( tmp_index_dir )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	216 ref_file_name = ref_file.name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	217 ref_file.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	218 os.symlink( options.ref, ref_file_name )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	219 cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	220 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	222 tmp_stderr = open( tmp, 'wb' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	223 proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	224 returncode = proc.wait()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	225 tmp_stderr.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	226 # get stderr, allowing for case where it's very large
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	227 tmp_stderr = open( tmp, 'rb' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 stderr = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	229 buffsize = 1048576
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	230 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	231 while True:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 stderr += tmp_stderr.read( buffsize )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233 if not stderr or len( stderr ) % buffsize != 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	234 break
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	235 except OverflowError:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	236 pass
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	237 tmp_stderr.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	238 if returncode != 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	239 raise Exception, stderr
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	240 except Exception, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 # clean up temp dir
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242 if os.path.exists( tmp_index_dir ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243 shutil.rmtree( tmp_index_dir )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 stop_err( 'Error indexing reference sequence\n' + str( e ) )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 stdout += 'File indexed. '
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 ref_file_name = options.ref
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 # set up aligning and generate aligning command options
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249 # automatically set threads in both cases
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 tmp_suppressed_file_name = None
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 tmp_unmapped_file_name = None
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252 if options.suppressHeader == 'true':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 suppressHeader = '--sam-nohead'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	254 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	255 suppressHeader = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 if options.maxInsert and int( options.maxInsert ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 maxInsert = '-X %s' % options.maxInsert
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	259 maxInsert = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	260 if options.mateOrient:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261 mateOrient = '--%s' % options.mateOrient
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 mateOrient = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	265 if options.params == 'preSet':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	266 aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	267 ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	268 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	269 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	270 if options.skip and int( options.skip ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	271 skip = '-s %s' % options.skip
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	272 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	273 skip = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	274 if options.alignLimit and int( options.alignLimit ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	275 alignLimit = '-u %s' % options.alignLimit
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	276 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	277 alignLimit = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	278 if options.trimH and int( options.trimH ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	279 trimH = '-5 %s' % options.trimH
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	280 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	281 trimH = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	282 if options.trimL and int( options.trimL ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	283 trimL = '-3 %s' % options.trimL
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	284 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	285 trimL = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	286 if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 maqSoapAlign = '-v %s' % options.maqSoapAlign
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	288 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	289 maqSoapAlign = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	290 if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	291 or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	292 mismatchSeed = '-n %s' % options.mismatchSeed
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	293 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	294 mismatchSeed = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	295 if options.mismatchQual and int( options.mismatchQual ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	296 mismatchQual = '-e %s' % options.mismatchQual
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	297 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	298 mismatchQual = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	299 if options.seedLen and int( options.seedLen ) >= 5:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 seedLen = '-l %s' % options.seedLen
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	301 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	302 seedLen = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	303 if options.rounding == 'noRound':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	304 rounding = '--nomaqround'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	305 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	306 rounding = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	307 if options.minInsert and int( options.minInsert ) > 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	308 minInsert = '-I %s' % options.minInsert
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	309 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	310 minInsert = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	311 if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 maxAlignAttempt = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	315 if options.forwardAlign == 'noForward':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	316 forwardAlign = '--nofw'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	317 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	318 forwardAlign = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	319 if options.reverseAlign == 'noReverse':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	320 reverseAlign = '--norc'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	321 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	322 reverseAlign = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	323 if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	324 ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	325 maxBacktracks = '--maxbts %s' % options.maxBacktracks
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327 maxBacktracks = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	328 if options.tryHard == 'doTryHard':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	329 tryHard = '-y'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	330 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	331 tryHard = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	332 if options.valAlign and int( options.valAlign ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	333 valAlign = '-k %s' % options.valAlign
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	334 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	335 valAlign = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	336 if options.allValAligns == 'doAllValAligns':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	337 allValAligns = '-a'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	338 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	339 allValAligns = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	340 if options.suppressAlign and int( options.suppressAlign ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	341 suppressAlign = '-m %s' % options.suppressAlign
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	342 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	343 suppressAlign = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	344 if options.best == 'doBest':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	345 best = '--best'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	346 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	347 best = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	348 if options.strata == 'doStrata':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	349 strata = '--strata'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	350 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	351 strata = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	352 if options.offrate and int( options.offrate ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	353 offrate = '-o %s' % options.offrate
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	354 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	355 offrate = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	356 if options.seed and int( options.seed ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	357 seed = '--seed %s' % options.seed
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	358 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	359 seed = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	360 if options.paired == 'paired':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	361 if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	362 tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	363 tmp_unmapped_file_name = tmp_unmapped_file.name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	364 tmp_unmapped_file.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	365 output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	366 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	367 output_unmapped_reads = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	368 if options.output_suppressed_reads:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	369 tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	370 tmp_suppressed_file_name = tmp_suppressed_file.name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	371 tmp_suppressed_file.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	372 output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	373 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	374 output_suppressed_reads = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	375 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	376 if options.output_unmapped_reads:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	377 output_unmapped_reads = '--un %s' % options.output_unmapped_reads
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	378 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	379 output_unmapped_reads = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	380 if options.output_suppressed_reads:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	381 output_suppressed_reads = '--max %s' % options.output_suppressed_reads
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	382 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	383 output_suppressed_reads = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	384 snpfrac = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	385 if options.snpphred and int( options.snpphred ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	386 snpphred = '--snpphred %s' % options.snpphred
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	387 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	388 snpphred = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	389 if options.snpfrac and float( options.snpfrac ) >= 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	390 snpfrac = '--snpfrac %s' % options.snpfrac
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	391 if options.keepends and options.keepends == 'doKeepends':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	392 keepends = '--col-keepends'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	393 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	394 keepends = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	395 aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	396 '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	397 ( maxInsert, mateOrient, options.threads, suppressHeader,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	398 colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	399 mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	400 maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	401 tryHard, valAlign, allValAligns, suppressAlign, best,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	402 strata, offrate, seed, snpphred, snpfrac, keepends,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	403 output_unmapped_reads, output_suppressed_reads,
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	404 quality_score_encoding )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	405 except ValueError, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	406 # clean up temp dir
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	407 if os.path.exists( tmp_index_dir ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	408 shutil.rmtree( tmp_index_dir )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	409 stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	410 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	411 # have to nest try-except in try-finally to handle 2.4
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	412 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	413 # prepare actual mapping commands
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	414 if options.paired == 'paired':
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	415 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	416 else:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	417 cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	418 # align
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	419 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	420 tmp_stderr = open( tmp, 'wb' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	421 proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	422 returncode = proc.wait()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	423 tmp_stderr.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	424 # get stderr, allowing for case where it's very large
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	425 tmp_stderr = open( tmp, 'rb' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	426 stderr = ''
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	427 buffsize = 1048576
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	428 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	429 while True:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	430 stderr += tmp_stderr.read( buffsize )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	431 if not stderr or len( stderr ) % buffsize != 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	432 break
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	433 except OverflowError:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	434 pass
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	435 tmp_stderr.close()
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	436 if returncode != 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	437 raise Exception, stderr
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	438 # get suppressed and unmapped reads output files in place if appropriate
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	439 if options.paired == 'paired' and tmp_suppressed_file_name and \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	440 options.output_suppressed_reads_l and options.output_suppressed_reads_r:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	441 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	442 left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	443 right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	444 shutil.move( left, options.output_suppressed_reads_l )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	445 shutil.move( right, options.output_suppressed_reads_r )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	446 except Exception, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	447 sys.stdout.write( 'Error producing the suppressed output file.\n' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	448 if options.paired == 'paired' and tmp_unmapped_file_name and \
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	449 options.output_unmapped_reads_l and options.output_unmapped_reads_r:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	450 try:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	451 left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	452 right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	453 shutil.move( left, options.output_unmapped_reads_l )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	454 shutil.move( right, options.output_unmapped_reads_r )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	455 except Exception, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	456 sys.stdout.write( 'Error producing the unmapped output file.\n' )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	457 # check that there are results in the output file
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	458 if os.path.getsize( options.output ) == 0:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	459 raise Exception, 'The output file is empty, there may be an error with your input file or settings.'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	460 except Exception, e:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	461 stop_err( 'Error aligning sequence. ' + str( e ) )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	462 finally:
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	463 # clean up temp dir
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	464 if os.path.exists( tmp_index_dir ):
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	465 shutil.rmtree( tmp_index_dir )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	466 stdout += 'Sequence file aligned.\n'
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	467 sys.stdout.write( stdout )
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	468
60661549b3e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_color_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	469 if __name__=="__main__": __main__()

Mercurial > repos > devteam > bowtie_color_wrappers

annotate bowtie_wrapper.py @ 0:60661549b3e3 draft default tip