defuse: defuse_results_to

annotate defuse_results_to_vcf.py @ 40:ed07bcc39f6e

Provide a matched tabular output

author	Jim Johnson <jj@umn.edu>
date	Wed, 06 May 2015 14:31:57 -0500
parents	3099cec648e7
children

rev	line source
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	1 #!/usr/bin/env python
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	2 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	3 #
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	4 #------------------------------------------------------------------------------
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	5 # University of Minnesota
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	6 # Copyright 2012, Regents of the University of Minnesota
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	7 #------------------------------------------------------------------------------
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	8 # Author:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	9 #
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	10 # James E Johnson
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	11 # Jesse Erdmann
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	12 #
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	13 #------------------------------------------------------------------------------
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	14 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	15
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	16
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	17 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	19 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	20
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	21 import sys,re,os.path
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	22 import optparse
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	23 from optparse import OptionParser
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	24
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	25 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	26 http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	27
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	28 5. INFO keys used for structural variants
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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).
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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).
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	31 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	32 ##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	33 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	34 For precise variants, END is POS + length of REF allele - 1, and the for imprecise variants the corresponding best estimate.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	35 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	37 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	39 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	40 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	41 ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	42 ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	43 ##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	45 ##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	46 ##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	47 ##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	48 ##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	49 ##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	50 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	51 ##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	52 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	53 ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the length of the inserted material between breakends">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	54 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	55 ##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	56 ##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	57 ##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	58 ##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	59 ##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	60 6. FORMAT keys used for structural variants
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	61 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	62 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	63 ##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	65 ##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	66 ##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	68
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	69 Specifying Complex Rearrangements with Breakends
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	70 An arbitrary rearrangement event can be summarized as a set of novel adjacencies.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	71 Each adjacency ties together 2 breakends. The two breakends at either end of a novel adjacency are called mates.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> 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:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	77 REF ALT Meaning
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	78 s t[p[ piece extending to the right of p is joined after t
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	79 s t]p] reverse comp piece extending left of p is joined after t
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	80 s ]p]t piece extending to the left of p is joined before t
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	81 s [p[t reverse comp piece extending right of p is joined before t
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	82
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	83 Examples:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	84 #CHROM POS ID REF ALT QUAL FILT INFO
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	85 2 321681 bnd_W G G]17:198982] 6 PASS SVTYPE=BND;MATEID=bnd_Y
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	86 2 321682 bnd_V T ]13:123456]T 6 PASS SVTYPE=BND;MATEID=bnd_U
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	87 13 123456 bnd_U C C[2:321682[ 6 PASS SVTYPE=BND;MATEID=bnd_V
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	88 13 123457 bnd_X A [17:198983[A 6 PASS SVTYPE=BND;MATEID=bnd_Z
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	89 17 198982 bnd_Y A A]2:321681] 6 PASS SVTYPE=BND;MATEID=bnd_W
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	90 17 198983 bnd_Z C [13:123457[C 6 PASS SVTYPE=BND;MATEID=bnd_X
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	91 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	92
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	93 vcf_header = """\
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	94 ##fileformat=VCFv4.1
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	95 ##source=defuse
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	96 ##reference=%s
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	97 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	98 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	99 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
34 3099cec648e7 Update tool_dependencies, add help Jim Johnson <jj@umn.edu> parents: 32 diff changeset	100 ##INFO=<ID=MATELOC,Number=1,Type=String,Description="The chrom:position of the BND mate">
3099cec648e7 Update tool_dependencies, add help Jim Johnson <jj@umn.edu> parents: 32 diff changeset	101 ##INFO=<ID=GENESTRAND,Number=2,Type=String,Description="Strands">
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	102 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	103 ##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	104 ##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	105 ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	106 ##INFO=<ID=SPLICESCORE,Number=1,Type=Integer,Description="number of nucleotides similar to GTAG at fusion splice">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	107 ##INFO=<ID=GENE,Number=2,Type=String,Description="Gene Names at each breakend">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	108 ##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs at each breakend">
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	109 ##INFO=<ID=GENELOC,Number=2,Type=String,Description="location of breakpoint releative to genes">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	110 ##INFO=<ID=EXPR,Number=2,Type=Integer,Description="expression of genes as number of concordant pairs aligned to exons">
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	111 ##INFO=<ID=ORF,Number=0,Type=Flag,Description="fusion combines genes in a way that preserves a reading frame">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	112 ##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	113 ##INFO=<ID=INTERCHROM,Number=0,Type=Flag,Description="fusion produced by an interchromosomal translocation">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	114 ##INFO=<ID=READTHROUGH,Number=0,Type=Flag,Description="fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	115 ##INFO=<ID=ADJACENT,Number=0,Type=Flag,Description="fusion between adjacent genes">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	116 ##INFO=<ID=ALTSPLICE,Number=0,Type=Flag,Description="fusion likely the product of alternative splicing between adjacent genes">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	117 ##INFO=<ID=DELETION,Number=0,Type=Flag,Description="fusion produced by a genomic deletion">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	118 ##INFO=<ID=EVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic eversion">
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	119 ##INFO=<ID=INVERSION,Number=0,Type=Flag,Description="fusion produced by a genomic inversion">
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	120 #CHROM POS ID REF ALT QUAL FILTER INFO\
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	121 """
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	122
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	123 def cmp_alphanumeric(s1,s2):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	124 if s1 == s2:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	125 return 0
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	126 a1 = re.findall("\d+\|[a-zA-Z]+",s1)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	127 a2 = re.findall("\d+\|[a-zA-Z]+",s2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	128 for i in range(min(len(a1),len(a2))):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	129 if a1[i] == a2[i]:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	130 continue
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	131 if a1[i].isdigit() and a2[i].isdigit():
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	132 return int(a1[i]) - int(a2[i])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	133 return 1 if a1[i] > a2[i] else -1
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	134 return len(a1) - len(a2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	135
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	136 def __main__():
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	137 # VCF functions
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	138 chr_dict = dict()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	139 def add_vcf_line(chr,pos,id,line):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	140 if chr not in chr_dict:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	141 pos_dict = dict()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	142 chr_dict[chr] = pos_dict
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	143 if pos not in chr_dict[chr]:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	144 id_dict = dict()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	145 chr_dict[chr][pos] = id_dict
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	146 chr_dict[chr][pos][id] = line
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	147
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	148 def write_vcf():
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	149 print >> outputFile, vcf_header % (refname)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	150 for chr in sorted(chr_dict.keys(),cmp=cmp_alphanumeric):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	151 for pos in sorted(chr_dict[chr].keys()):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	152 for id in chr_dict[chr][pos]:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	153 print >> outputFile, chr_dict[chr][pos][id]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	154 #Parse Command Line
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	155 parser = optparse.OptionParser()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	156 # files
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	157 parser.add_option( '-i', '--input', dest='input', help='The input defuse results.tsv file (else read from stdin)' )
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	158 parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	159 parser.add_option( '-r', '--reference', dest='reference', default=None, help='The genomic reference id' )
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	160 (options, args) = parser.parse_args()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	161
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	162 # results.tsv input
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	163 if options.input != None:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	164 try:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	165 inputPath = os.path.abspath(options.input)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	166 inputFile = open(inputPath, 'r')
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	167 except Exception, e:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	168 print >> sys.stderr, "failed: %s" % e
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	169 exit(2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	170 else:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	171 inputFile = sys.stdin
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	172 # vcf output
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	173 if options.output != None:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	174 try:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	175 outputPath = os.path.abspath(options.output)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	176 outputFile = open(outputPath, 'w')
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	177 except Exception, e:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	178 print >> sys.stderr, "failed: %s" % e
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	179 exit(3)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	180 else:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	181 outputFile = sys.stdout
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	182
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	183 refname = options.reference if options.reference else 'unknown'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	184
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	185 svtype = 'SVTYPE=BND'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	186 filt = 'PASS'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	187 columns = []
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	188 try:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	189 for linenum,line in enumerate(inputFile):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	190 ## print >> sys.stderr, "%d: %s\n" % (linenum,line)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	191 fields = line.strip().split('\t')
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	192 if line.startswith('cluster_id'):
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	193 columns = fields
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	194 ## print >> sys.stderr, "columns: %s\n" % columns
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	195 continue
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	196 cluster_id = fields[columns.index('cluster_id')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	197 gene_chromosome1 = fields[columns.index('gene_chromosome1')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	198 gene_chromosome2 = fields[columns.index('gene_chromosome2')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	199 genomic_strand1 = fields[columns.index('genomic_strand1')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	200 genomic_strand2 = fields[columns.index('genomic_strand2')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	201 gene1 = fields[columns.index('gene1')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	202 gene2 = fields[columns.index('gene2')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	203 gene_info = 'GENEID=%s,%s' % (gene1,gene2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	204 gene_name1 = fields[columns.index('gene_name1')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	205 gene_name2 = fields[columns.index('gene_name2')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	206 gene_name_info = 'GENE=%s,%s' % (gene_name1,gene_name2)
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	207 gene_location1 = fields[columns.index('gene_location1')]
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	208 gene_location2 = fields[columns.index('gene_location2')]
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	209 gene_loc = 'GENELOC=%s,%s' % (gene_location1,gene_location2)
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	210 expression1 = int(fields[columns.index('expression1')])
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	211 expression2 = int(fields[columns.index('expression2')])
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	212 expr = 'EXPR=%d,%d' % (expression1,expression2)
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	213 genomic_break_pos1 = int(fields[columns.index('genomic_break_pos1')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	214 genomic_break_pos2 = int(fields[columns.index('genomic_break_pos2')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	215 breakpoint_homology = int(fields[columns.index('breakpoint_homology')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	216 homlen = 'HOMLEN=%s' % breakpoint_homology
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	217 orf = fields[columns.index('orf')] == 'Y'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	218 exonboundaries = fields[columns.index('exonboundaries')] == 'Y'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	219 read_through = fields[columns.index('read_through')] == 'Y'
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	220 interchromosomal = fields[columns.index('interchromosomal')] == 'Y'
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	221 adjacent = fields[columns.index('adjacent')] == 'Y'
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	222 altsplice = fields[columns.index('altsplice')] == 'Y'
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	223 deletion = fields[columns.index('deletion')] == 'Y'
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	224 eversion = fields[columns.index('eversion')] == 'Y'
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	225 inversion = fields[columns.index('inversion')] == 'Y'
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	226 span_count = int(fields[columns.index('span_count')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	227 splitr_count = int(fields[columns.index('splitr_count')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	228 splice_score = int(fields[columns.index('splice_score')])
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	229 probability = fields[columns.index('probability')] if columns.index('probability') else '.'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	230 splitr_sequence = fields[columns.index('splitr_sequence')]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	231 split_seqs = splitr_sequence.split('\|')
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	232 mate_id1 = "bnd_%s_1" % cluster_id
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	233 mate_id2 = "bnd_%s_2" % cluster_id
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	234 ref1 = split_seqs[0][-1]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	235 ref2 = split_seqs[1][0]
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	236 b1 = '[' if genomic_strand1 == '+' else ']'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	237 b2 = '[' if genomic_strand2 == '+' else ']'
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	238 alt1 = "%s%s%s:%d%s" % (ref1,b2,gene_chromosome2,genomic_break_pos2,b2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	239 alt2 = "%s%s:%d%s%s" % (b1,gene_chromosome1,genomic_break_pos1,b1,ref2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	240 #TODO evaluate what should be included in the INFO field
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 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]
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	242 if orf:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	243 info.append('ORF')
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	244 if exonboundaries:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	245 info.append('EXONBND')
27 d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	246 if interchromosomal:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	247 info.append('INTERCHROM')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	248 if read_through:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	249 info.append('READTHROUGH')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	250 if adjacent:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	251 info.append('ADJACENT')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	252 if altsplice:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	253 info.append('ALTSPLICE')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	254 if deletion:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	255 info.append('DELETION')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	256 if eversion:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	257 info.append('EVERSION')
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	258 if inversion:
d57fcac025e2 Add more info fields to defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 25 diff changeset	259 info.append('INVERSION')
34 3099cec648e7 Update tool_dependencies, add help Jim Johnson <jj@umn.edu> parents: 32 diff changeset	260 info1 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id2,gene_chromosome2,genomic_break_pos2)] + info
3099cec648e7 Update tool_dependencies, add help Jim Johnson <jj@umn.edu> parents: 32 diff changeset	261 info2 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id1,gene_chromosome1,genomic_break_pos1)] + info
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	262 qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
32 8027fc53f3f9 Fix formatting error in defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 28 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) )
8027fc53f3f9 Fix formatting error in defuse_results_to_vcf.py Jim Johnson <jj@umn.edu> parents: 28 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) )
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	265 add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	266 add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2)
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	267 write_vcf()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	268 except Exception, e:
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	269 print >> sys.stderr, "failed: %s" % e
34 3099cec648e7 Update tool_dependencies, add help Jim Johnson <jj@umn.edu> parents: 32 diff changeset	270 sys.exit(1)
25 2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	271
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	272 if __name__ == "__main__" : __main__()
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results Jim Johnson <jj@umn.edu> parents: diff changeset	273

Mercurial > repos > jjohnson > defuse

annotate defuse_results_to_vcf.py @ 40:ed07bcc39f6e