defuse: defuse_results_to

annotate defuse_results_to_vcf.py @ 25:2ecf82136986

Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results

author	Jim Johnson <jj@umn.edu>
date	Fri, 09 Aug 2013 11:19:26 -0500
parents
children	d57fcac025e2

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">
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	100 ##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	101 ##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	102 ##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	103 ##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	104 ##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	105 ##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	106 ##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs 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	107 ##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	108 ##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
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	109 #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	110 """
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
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 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	113 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	114 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	115 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	116 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	117 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	118 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	119 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	120 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	121 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	122 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	123 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	124
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 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	126 # 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	127 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	128 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	129 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	130 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	131 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	132 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	133 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	134 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	135 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	136
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 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	138 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	139 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	140 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	141 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	142 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	143 #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	144 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	145 # 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	146 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	147 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	148 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	149 (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	150
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 # 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	152 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	153 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	154 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	155 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	156 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	157 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	158 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	159 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	160 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	161 # 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	162 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	163 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	164 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	165 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	166 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	167 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	168 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	169 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	170 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	171
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 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	173
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 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	175 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	176 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	177 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	178 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	179 ## 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	180 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	181 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	182 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	183 ## 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	184 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	185 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	186 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	187 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	188 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	189 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	190 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	191 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	192 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	193 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	194 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	195 gene_name_info = 'GENE=%s,%s' % (gene_name1,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	196 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	197 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	198 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	199 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	200 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	201 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	202 read_through = fields[columns.index('read_through')] == '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	203 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	204 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	205 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	206 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	207 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	208 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	209 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	210 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	211 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	212 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	213 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	214 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	215 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	216 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	217 #TODO evaluate what should be included in the INFO field
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 info = ['DP=%d' % (span_count + splitr_count),'SPLITCNT=%d' % splitr_count,'SPANCNT=%d' % span_count,gene_name_info,gene_info,homlen,'SPLICESCORE=%d' % 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	219 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	220 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	221 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	222 info.append('EXONBND')
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	223 info1 = [svtype,'MATEID=%s' % mate_id2] + 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	224 info2 = [svtype,'MATEID=%s' % mate_id1] + 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	225 qual = int(float(fields[columns.index('probability')]) * 255) 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	226 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) )
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 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) )
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 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	229 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	230 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	231 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	232 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	233 exit(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	234
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 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	236

Mercurial > repos > jjohnson > defuse

annotate defuse_results_to_vcf.py @ 25:2ecf82136986