defuse: defuse_results_to

annotate defuse_results_to_vcf.py @ 13:3a4876d01c7e draft

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author	jjohnson
date	Tue, 12 Dec 2017 10:01:42 -0500
parents	b22f8634ff84
children

rev	line source
11 b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	1 #!/usr/bin/env python
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	2 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	3 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	4 #------------------------------------------------------------------------------
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	5 # University of Minnesota
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	6 # Copyright 2012, Regents of the University of Minnesota
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	7 #------------------------------------------------------------------------------
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	8 # Author:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	9 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	10 # James E Johnson
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	11 # Jesse Erdmann
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	12 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	13 #------------------------------------------------------------------------------
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	14 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	15
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	16
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	17 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	18 This tool takes the defuse results.tsv tab-delimited file as input and creates a Variant Call Format file as output.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	19 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	20
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	21 import sys,re,os.path
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	22 import optparse
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	23 from optparse import OptionParser
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	24
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	25 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	26 http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	27
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	28 5. INFO keys used for structural variants
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	29 When the INFO keys reserved for encoding structural variants are used for imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	30 The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	31 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	32 ##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	33 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	34 For precise variants, END is POS + length of REF allele - 1, and the for imprecise variants the corresponding best estimate.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	35 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	36 Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can be derived from the REF/ALT fields but is useful for filtering.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	37 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	38 One value for each ALT allele. Longer ALT alleles (e.g. insertions) have positive values, shorter ALT alleles (e.g. deletions) have negative values.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	39 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	40 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	41 ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	42 ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	43 ##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	44 For precise variants, the consensus sequence the alternate allele assembly is derivable from the REF and ALT fields. However, the alternate allele assembly file may contain additional information about the characteristics of the alt allele contigs.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	45 ##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	46 ##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	47 ##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	48 ##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	49 ##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	50 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	51 ##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	52 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	53 ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the length of the inserted material between breakends">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	54 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	55 ##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	56 ##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	57 ##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	58 ##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	59 ##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	60 6. FORMAT keys used for structural variants
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	61 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	62 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	63 ##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	64 ##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel with respect to the genome's ancestor">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	65 ##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	66 ##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	67 These keys are analogous to GT/GQ/GL and are provided for genotyping imprecise events by copy number (either because there is an unknown number of alternate alleles or because the haplotypes cannot be determined). CN specifies the integer copy number of the variant in this sample. CNQ is encoded as a phred quality -10log_10p(copy number genotype call is wrong). CNL specifies a list of log10 likelihoods for each potential copy number, starting from zero. When possible, GT/GQ/GL should be used instead of (or in addition to) these keys.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	68
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	69 Specifying Complex Rearrangements with Breakends
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	70 An arbitrary rearrangement event can be summarized as a set of novel adjacencies.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	71 Each adjacency ties together 2 breakends. The two breakends at either end of a novel adjacency are called mates.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	72 There is one line of VCF (i.e. one record) for each of the two breakends in a novel adjacency. A breakend record is identified with the tag SYTYPE=BND" in the INFO field. The REF field of a breakend record indicates a base or sequence s of bases beginning at position POS, as in all VCF records. The ALT field of a breakend record indicates a replacement for s. This "breakend replacement" has three parts:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	73 the string t that replaces places s. The string t may be an extended version of s if some novel bases are inserted during the formation of the novel adjacency.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	74 The position p of the mate breakend, indicated by a string of the form "chr:pos". This is the location of the first mapped base in the piece being joined at this novel adjacency.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	75 The direction that the joined sequence continues in, starting from p. This is indicated by the orientation of square brackets surrounding p.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	76 These 3 elements are combined in 4 possible ways to create the ALT. In each of the 4 cases, the assertion is that s is replaced with t, and then some piece starting at position p is joined to t. The cases are:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	77 REF ALT Meaning
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	78 s t[p[ piece extending to the right of p is joined after t
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	79 s t]p] reverse comp piece extending left of p is joined after t
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	80 s ]p]t piece extending to the left of p is joined before t
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	81 s [p[t reverse comp piece extending right of p is joined before t
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	82
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	83 Examples:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	84 #CHROM POS ID REF ALT QUAL FILT INFO
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	85 2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND;MATEID=bnd_Y
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	86 2 321682 bnd_V T ]13:123456]T 6 PASS SVTYPE=BND;MATEID=bnd_U
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	87 13 123456 bnd_U C C[2:321682[ 6 PASS SVTYPE=BND;MATEID=bnd_V
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	88 13 123457 bnd_X A [17:198983[A 6 PASS SVTYPE=BND;MATEID=bnd_Z
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	89 17 198982 bnd_Y A A]2:321681] 6 PASS SVTYPE=BND;MATEID=bnd_W
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	90 17 198983 bnd_Z C [13:123457[C 6 PASS SVTYPE=BND;MATEID=bnd_X
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	91 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	92
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	93 vcf_header = """\
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	94 ##fileformat=VCFv4.1
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	95 ##source=defuse
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	96 ##reference=%s
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	97 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	98 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	99 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	100 ##INFO=<ID=MATELOC,Number=1,Type=String,Description="The chrom:position of the BND mate">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	101 ##INFO=<ID=GENESTRAND,Number=2,Type=String,Description="Strands">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	102 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	103 ##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	104 ##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	105 ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	106 ##INFO=<ID=SPLICESCORE,Number=1,Type=Integer,Description="number of nucleotides similar to GTAG at fusion splice">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	107 ##INFO=<ID=GENE,Number=2,Type=String,Description="Gene Names at each breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	108 ##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs at each breakend">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	109 ##INFO=<ID=GENELOC,Number=2,Type=String,Description="location of breakpoint releative to genes">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	110 ##INFO=<ID=EXPR,Number=2,Type=Integer,Description="expression of genes as number of concordant pairs aligned to exons">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	111 ##INFO=<ID=ORF,Number=0,Type=Flag,Description="fusion combines genes in a way that preserves a reading frame">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	112 ##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	113 ##INFO=<ID=INTERCHROM,Number=0,Type=Flag,Description="fusion produced by an interchromosomal translocation">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	114 ##INFO=<ID=READTHROUGH,Number=0,Type=Flag,Description="fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	115 ##INFO=<ID=ADJACENT,Number=0,Type=Flag,Description="fusion between adjacent genes">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	116 ##INFO=<ID=ALTSPLICE,Number=0,Type=Flag,Description="fusion likely the product of alternative splicing between adjacent genes">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	117 ##INFO=<ID=DELETION,Number=0,Type=Flag,Description="fusion produced by a genomic deletion">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	118 ##INFO=<ID=EVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic eversion">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	119 ##INFO=<ID=INVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic inversion">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	120 #CHROM POS ID REF ALT QUAL FILTER INFO\
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	121 """
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	122
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	123 def cmp_alphanumeric(s1,s2):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	124 if s1 == s2:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	125 return 0
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	126 a1 = re.findall("\d+\|[a-zA-Z]+",s1)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	127 a2 = re.findall("\d+\|[a-zA-Z]+",s2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	128 for i in range(min(len(a1),len(a2))):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	129 if a1[i] == a2[i]:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	130 continue
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	131 if a1[i].isdigit() and a2[i].isdigit():
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	132 return int(a1[i]) - int(a2[i])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	133 return 1 if a1[i] > a2[i] else -1
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	134 return len(a1) - len(a2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	135
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	136 def __main__():
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	137 # VCF functions
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	138 chr_dict = dict()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	139 def add_vcf_line(chr,pos,id,line):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	140 if chr not in chr_dict:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	141 pos_dict = dict()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	142 chr_dict[chr] = pos_dict
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	143 if pos not in chr_dict[chr]:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	144 id_dict = dict()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	145 chr_dict[chr][pos] = id_dict
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	146 chr_dict[chr][pos][id] = line
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	147
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	148 def write_vcf():
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	149 print >> outputFile, vcf_header % (refname)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	150 for chr in sorted(chr_dict.keys(),cmp=cmp_alphanumeric):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	151 for pos in sorted(chr_dict[chr].keys()):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	152 for id in chr_dict[chr][pos]:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	153 print >> outputFile, chr_dict[chr][pos][id]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	154 #Parse Command Line
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	155 parser = optparse.OptionParser()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	156 # files
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	157 parser.add_option( '-i', '--input', dest='input', help='The input defuse results.tsv file (else read from stdin)' )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	158 parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	159 parser.add_option( '-r', '--reference', dest='reference', default=None, help='The genomic reference id' )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	160 (options, args) = parser.parse_args()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	161
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	162 # results.tsv input
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	163 if options.input != None:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	164 try:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	165 inputPath = os.path.abspath(options.input)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	166 inputFile = open(inputPath, 'r')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	167 except Exception, e:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	168 print >> sys.stderr, "failed: %s" % e
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	169 exit(2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	170 else:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	171 inputFile = sys.stdin
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	172 # vcf output
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	173 if options.output != None:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	174 try:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	175 outputPath = os.path.abspath(options.output)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	176 outputFile = open(outputPath, 'w')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	177 except Exception, e:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	178 print >> sys.stderr, "failed: %s" % e
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	179 exit(3)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	180 else:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	181 outputFile = sys.stdout
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	182
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	183 refname = options.reference if options.reference else 'unknown'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	184
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	185 svtype = 'SVTYPE=BND'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	186 filt = 'PASS'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	187 columns = []
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	188 try:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	189 for linenum,line in enumerate(inputFile):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	190 ## print >> sys.stderr, "%d: %s\n" % (linenum,line)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	191 fields = line.strip().split('\t')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	192 if line.startswith('cluster_id'):
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	193 columns = fields
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	194 ## print >> sys.stderr, "columns: %s\n" % columns
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	195 continue
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	196 cluster_id = fields[columns.index('cluster_id')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	197 gene_chromosome1 = fields[columns.index('gene_chromosome1')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	198 gene_chromosome2 = fields[columns.index('gene_chromosome2')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	199 genomic_strand1 = fields[columns.index('genomic_strand1')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	200 genomic_strand2 = fields[columns.index('genomic_strand2')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	201 gene1 = fields[columns.index('gene1')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	202 gene2 = fields[columns.index('gene2')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	203 gene_info = 'GENEID=%s,%s' % (gene1,gene2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	204 gene_name1 = fields[columns.index('gene_name1')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	205 gene_name2 = fields[columns.index('gene_name2')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	206 gene_name_info = 'GENE=%s,%s' % (gene_name1,gene_name2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	207 gene_location1 = fields[columns.index('gene_location1')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	208 gene_location2 = fields[columns.index('gene_location2')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	209 gene_loc = 'GENELOC=%s,%s' % (gene_location1,gene_location2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	210 expression1 = int(fields[columns.index('expression1')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	211 expression2 = int(fields[columns.index('expression2')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	212 expr = 'EXPR=%d,%d' % (expression1,expression2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	213 genomic_break_pos1 = int(fields[columns.index('genomic_break_pos1')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	214 genomic_break_pos2 = int(fields[columns.index('genomic_break_pos2')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	215 breakpoint_homology = int(fields[columns.index('breakpoint_homology')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	216 homlen = 'HOMLEN=%s' % breakpoint_homology
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	217 orf = fields[columns.index('orf')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	218 exonboundaries = fields[columns.index('exonboundaries')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	219 read_through = fields[columns.index('read_through')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	220 interchromosomal = fields[columns.index('interchromosomal')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	221 adjacent = fields[columns.index('adjacent')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	222 altsplice = fields[columns.index('altsplice')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	223 deletion = fields[columns.index('deletion')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	224 eversion = fields[columns.index('eversion')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	225 inversion = fields[columns.index('inversion')] == 'Y'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	226 span_count = int(fields[columns.index('span_count')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	227 splitr_count = int(fields[columns.index('splitr_count')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	228 splice_score = int(fields[columns.index('splice_score')])
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	229 probability = fields[columns.index('probability')] if columns.index('probability') else '.'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	230 splitr_sequence = fields[columns.index('splitr_sequence')]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	231 split_seqs = splitr_sequence.split('\|')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	232 mate_id1 = "bnd_%s_1" % cluster_id
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	233 mate_id2 = "bnd_%s_2" % cluster_id
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	234 ref1 = split_seqs[0][-1]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	235 ref2 = split_seqs[1][0]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	236 b1 = '[' if genomic_strand1 == '+' else ']'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	237 b2 = '[' if genomic_strand2 == '+' else ']'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	238 alt1 = "%s%s%s:%d%s" % (ref1,b2,gene_chromosome2,genomic_break_pos2,b2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	239 alt2 = "%s%s:%d%s%s" % (b1,gene_chromosome1,genomic_break_pos1,b1,ref2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	240 #TODO evaluate what should be included in the INFO field
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	241 info = ['DP=%d' % (span_count + splitr_count),'SPLITCNT=%d' % splitr_count,'SPANCNT=%d' % span_count,gene_name_info,gene_info,gene_loc,expr,homlen,'SPLICESCORE=%d' % splice_score]
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	242 if orf:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	243 info.append('ORF')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	244 if exonboundaries:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	245 info.append('EXONBND')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	246 if interchromosomal:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	247 info.append('INTERCHROM')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	248 if read_through:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	249 info.append('READTHROUGH')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	250 if adjacent:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	251 info.append('ADJACENT')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	252 if altsplice:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	253 info.append('ALTSPLICE')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	254 if deletion:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	255 info.append('DELETION')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	256 if eversion:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	257 info.append('EVERSION')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	258 if inversion:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	259 info.append('INVERSION')
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	260 info1 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id2,gene_chromosome2,genomic_break_pos2)] + info
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	261 info2 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id1,gene_chromosome1,genomic_break_pos1)] + info
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	262 qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	263 vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	264 vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	265 add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	266 add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	267 write_vcf()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	268 except Exception, e:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	269 print >> sys.stderr, "failed: %s" % e
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	270 sys.exit(1)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	271
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	272 if __name__ == "__main__" : __main__()
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty jjohnson parents: diff changeset	273

Mercurial > repos > jjohnson > defuse

annotate defuse_results_to_vcf.py @ 13:3a4876d01c7e draft