defuse8: defuse_results_to

annotate defuse_results_to_vcf.py @ 1:e0a835a2f74a draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 1a82c0609363fe0541e6dbdd46308a67f30ca9e1-dirty

author	jjohnson
date	Mon, 20 May 2019 15:30:06 -0400
parents	63f23d5db27c
children

rev	line source
0 63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	1 #!/usr/bin/env python
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	2 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	3 #
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	4 #------------------------------------------------------------------------------
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	5 # University of Minnesota
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	6 # Copyright 2012, Regents of the University of Minnesota
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	7 #------------------------------------------------------------------------------
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	8 # Author:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	9 #
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	10 # James E Johnson
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	11 # Jesse Erdmann
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	12 #
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	13 #------------------------------------------------------------------------------
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	14 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	15
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	16
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	17 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	19 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	20
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	21 import sys,re,os.path
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	22 import optparse
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	23 from optparse import OptionParser
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	24
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	25 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	26 http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	27
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	28 5. INFO keys used for structural variants
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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).
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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).
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	31 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	32 ##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	33 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	35 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	37 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	39 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	40 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	41 ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	42 ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	43 ##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	45 ##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	47 ##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	48 ##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	49 ##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	50 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	51 ##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	52 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	54 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	55 ##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	56 ##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	57 ##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	58 ##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	59 ##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	60 6. FORMAT keys used for structural variants
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	61 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	62 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	63 ##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	65 ##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	66 ##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	68
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	69 Specifying Complex Rearrangements with Breakends
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	70 An arbitrary rearrangement event can be summarized as a set of novel adjacencies.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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.
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	77 REF ALT Meaning
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	78 s t[p[ piece extending to the right of p is joined after t
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	79 s t]p] reverse comp piece extending left of p is joined after t
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	80 s ]p]t piece extending to the left of p is joined before t
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	81 s [p[t reverse comp piece extending right of p is joined before t
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	82
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	83 Examples:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	84 #CHROM POS ID REF ALT QUAL FILT INFO
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	85 2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND;MATEID=bnd_Y
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	86 2 321682 bnd_V T ]13:123456]T 6 PASS SVTYPE=BND;MATEID=bnd_U
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	87 13 123456 bnd_U C C[2:321682[ 6 PASS SVTYPE=BND;MATEID=bnd_V
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	88 13 123457 bnd_X A [17:198983[A 6 PASS SVTYPE=BND;MATEID=bnd_Z
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	89 17 198982 bnd_Y A A]2:321681] 6 PASS SVTYPE=BND;MATEID=bnd_W
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	90 17 198983 bnd_Z C [13:123457[C 6 PASS SVTYPE=BND;MATEID=bnd_X
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	91 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	92
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	93 vcf_header = """\
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	94 ##fileformat=VCFv4.1
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	95 ##source=defuse
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	96 ##reference=%s
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	97 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	98 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	99 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	100 ##INFO=<ID=MATELOC,Number=1,Type=String,Description="The chrom:position of the BND mate">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	101 ##INFO=<ID=GENESTRAND,Number=2,Type=String,Description="Strands">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	102 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	103 ##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	104 ##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	105 ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	106 ##INFO=<ID=SPLICESCORE,Number=1,Type=Integer,Description="number of nucleotides similar to GTAG at fusion splice">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	107 ##INFO=<ID=GENE,Number=2,Type=String,Description="Gene Names at each breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	108 ##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs at each breakend">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	109 ##INFO=<ID=GENELOC,Number=2,Type=String,Description="location of breakpoint releative to genes">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	112 ##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	113 ##INFO=<ID=INTERCHROM,Number=0,Type=Flag,Description="fusion produced by an interchromosomal translocation">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	115 ##INFO=<ID=ADJACENT,Number=0,Type=Flag,Description="fusion between adjacent genes">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	116 ##INFO=<ID=ALTSPLICE,Number=0,Type=Flag,Description="fusion likely the product of alternative splicing between adjacent genes">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	117 ##INFO=<ID=DELETION,Number=0,Type=Flag,Description="fusion produced by a genomic deletion">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	118 ##INFO=<ID=EVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic eversion">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	119 ##INFO=<ID=INVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic inversion">
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	120 #CHROM POS ID REF ALT QUAL FILTER INFO\
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	121 """
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	122
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	123 def cmp_alphanumeric(s1,s2):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	124 if s1 == s2:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	125 return 0
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	126 a1 = re.findall("\d+\|[a-zA-Z]+",s1)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	127 a2 = re.findall("\d+\|[a-zA-Z]+",s2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	128 for i in range(min(len(a1),len(a2))):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	129 if a1[i] == a2[i]:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	130 continue
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	131 if a1[i].isdigit() and a2[i].isdigit():
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	132 return int(a1[i]) - int(a2[i])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	133 return 1 if a1[i] > a2[i] else -1
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	134 return len(a1) - len(a2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	135
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	136 def __main__():
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	137 # VCF functions
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	138 chr_dict = dict()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	139 def add_vcf_line(chr,pos,id,line):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	140 if chr not in chr_dict:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	141 pos_dict = dict()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	142 chr_dict[chr] = pos_dict
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	143 if pos not in chr_dict[chr]:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	144 id_dict = dict()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	145 chr_dict[chr][pos] = id_dict
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	146 chr_dict[chr][pos][id] = line
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	147
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	148 def write_vcf():
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	149 print >> outputFile, vcf_header % (refname)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	150 for chr in sorted(chr_dict.keys(),cmp=cmp_alphanumeric):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	151 for pos in sorted(chr_dict[chr].keys()):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	152 for id in chr_dict[chr][pos]:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	153 print >> outputFile, chr_dict[chr][pos][id]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	154 #Parse Command Line
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	155 parser = optparse.OptionParser()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	156 # files
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	157 parser.add_option( '-i', '--input', dest='input', help='The input defuse results.tsv file (else read from stdin)' )
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	158 parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	159 parser.add_option( '-r', '--reference', dest='reference', default=None, help='The genomic reference id' )
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	160 (options, args) = parser.parse_args()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	161
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	162 # results.tsv input
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	163 if options.input != None:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	164 try:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	165 inputPath = os.path.abspath(options.input)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	166 inputFile = open(inputPath, 'r')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	167 except Exception, e:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	168 print >> sys.stderr, "failed: %s" % e
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	169 exit(2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	170 else:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	171 inputFile = sys.stdin
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	172 # vcf output
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	173 if options.output != None:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	174 try:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	175 outputPath = os.path.abspath(options.output)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	176 outputFile = open(outputPath, 'w')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	177 except Exception, e:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	178 print >> sys.stderr, "failed: %s" % e
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	179 exit(3)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	180 else:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	181 outputFile = sys.stdout
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	182
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	183 refname = options.reference if options.reference else 'unknown'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	184
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	185 svtype = 'SVTYPE=BND'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	186 filt = 'PASS'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	187 columns = []
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	188 try:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	189 for linenum,line in enumerate(inputFile):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	190 ## print >> sys.stderr, "%d: %s\n" % (linenum,line)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	191 fields = line.strip().split('\t')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	192 if line.startswith('cluster_id'):
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	193 columns = fields
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	194 ## print >> sys.stderr, "columns: %s\n" % columns
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	195 continue
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	196 cluster_id = fields[columns.index('cluster_id')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	197 gene_chromosome1 = fields[columns.index('gene_chromosome1')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	198 gene_chromosome2 = fields[columns.index('gene_chromosome2')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	199 genomic_strand1 = fields[columns.index('genomic_strand1')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	200 genomic_strand2 = fields[columns.index('genomic_strand2')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	201 gene1 = fields[columns.index('gene1')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	202 gene2 = fields[columns.index('gene2')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	203 gene_info = 'GENEID=%s,%s' % (gene1,gene2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	204 gene_name1 = fields[columns.index('gene_name1')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	205 gene_name2 = fields[columns.index('gene_name2')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	206 gene_name_info = 'GENE=%s,%s' % (gene_name1,gene_name2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	207 gene_location1 = fields[columns.index('gene_location1')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	208 gene_location2 = fields[columns.index('gene_location2')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	209 gene_loc = 'GENELOC=%s,%s' % (gene_location1,gene_location2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	210 expression1 = int(fields[columns.index('expression1')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	211 expression2 = int(fields[columns.index('expression2')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	212 expr = 'EXPR=%d,%d' % (expression1,expression2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	213 genomic_break_pos1 = int(fields[columns.index('genomic_break_pos1')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	214 genomic_break_pos2 = int(fields[columns.index('genomic_break_pos2')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	215 breakpoint_homology = int(fields[columns.index('breakpoint_homology')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	216 homlen = 'HOMLEN=%s' % breakpoint_homology
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	217 orf = fields[columns.index('orf')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	218 exonboundaries = fields[columns.index('exonboundaries')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	219 read_through = fields[columns.index('read_through')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	220 interchromosomal = fields[columns.index('interchromosomal')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	221 adjacent = fields[columns.index('adjacent')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	222 altsplice = fields[columns.index('altsplice')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	223 deletion = fields[columns.index('deletion')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	224 eversion = fields[columns.index('eversion')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	225 inversion = fields[columns.index('inversion')] == 'Y'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	226 span_count = int(fields[columns.index('span_count')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	227 splitr_count = int(fields[columns.index('splitr_count')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	228 splice_score = int(fields[columns.index('splice_score')])
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	229 probability = fields[columns.index('probability')] if columns.index('probability') else '.'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	230 splitr_sequence = fields[columns.index('splitr_sequence')]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	231 split_seqs = splitr_sequence.split('\|')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	232 mate_id1 = "bnd_%s_1" % cluster_id
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	233 mate_id2 = "bnd_%s_2" % cluster_id
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	234 ref1 = split_seqs[0][-1]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	235 ref2 = split_seqs[1][0]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	236 b1 = '[' if genomic_strand1 == '+' else ']'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	237 b2 = '[' if genomic_strand2 == '+' else ']'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	238 alt1 = "%s%s%s:%d%s" % (ref1,b2,gene_chromosome2,genomic_break_pos2,b2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	239 alt2 = "%s%s:%d%s%s" % (b1,gene_chromosome1,genomic_break_pos1,b1,ref2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	240 #TODO evaluate what should be included in the INFO field
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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]
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	242 if orf:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	243 info.append('ORF')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	244 if exonboundaries:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	245 info.append('EXONBND')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	246 if interchromosomal:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	247 info.append('INTERCHROM')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	248 if read_through:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	249 info.append('READTHROUGH')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	250 if adjacent:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	251 info.append('ADJACENT')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	252 if altsplice:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	253 info.append('ALTSPLICE')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	254 if deletion:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	255 info.append('DELETION')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	256 if eversion:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	257 info.append('EVERSION')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	258 if inversion:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	259 info.append('INVERSION')
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	260 info1 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id2,gene_chromosome2,genomic_break_pos2)] + info
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	261 info2 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id1,gene_chromosome1,genomic_break_pos1)] + info
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	262 qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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) )
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-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) )
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	265 add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	266 add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	267 write_vcf()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	268 except Exception, e:
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	269 print >> sys.stderr, "failed: %s" % e
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	270 sys.exit(1)
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	271
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	272 if __name__ == "__main__" : __main__()
63f23d5db27c planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty jjohnson parents: diff changeset	273

Mercurial > repos > jjohnson > defuse8

annotate defuse_results_to_vcf.py @ 1:e0a835a2f74a draft default tip