A brute-force script to convert Syzygy lod-score calls files into a proper VCF -- with some useful annotations.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2261 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
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#!/usr/bin/env python
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#import farm_commands
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import subprocess
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import os
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import sys
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import re
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import time
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import math
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dbsnp = "." # can be global. Let something else annotate dbsnp info
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filter = "0" # don't declare any filtering in the VCF file
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print(sys.argv)
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raw_calls_file = open(sys.argv[1])
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output_vcf_file = open(sys.argv[2],'w')
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pool_name = []
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try:
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pool_name = sys.argv[3]
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except IndexError:
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# parse the file name
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filepath = sys.argv[0].strip().split("/")
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pool_name = filepath[len(filepath)]
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header = raw_calls_file.readline().strip()
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fields = header.split()
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print(fields)
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# parse it for important offsets
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chrompos = fields.index("chr:offset")
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ref_offset = fields.index("ref_base")
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for_a_index = fields.index("A")
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for_c_index = fields.index("C")
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for_g_index = fields.index("G")
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for_t_index = fields.index("T")
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for_d_index = fields.index("D")
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for_i_index = fields.index("I")
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for_depth_index = fields.index("sum")
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rev_a_index = fields.index("AR")
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rev_c_index = fields.index("CR")
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rev_g_index = fields.index("GR")
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rev_t_index = fields.index("TR")
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rev_d_index = fields.index("DR")
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rev_i_index = fields.index("IR")
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rev_depth_index = fields.index("sumr")
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total_depth_index = fields.index("combined_sum")
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lod_score_index = fields.index("combined_lod")
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call_index = fields.index("allele2")
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fish_flag = fields.index("flag")
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fish_pval_index = fields.index("fisher-pval")
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# now print the VCF header
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head1 = "##source=Syzygy"
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head2 = "##format=VCRv3.2"
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fields = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT",pool_name]
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head3 = "#" + "\t".join(fields)
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output_vcf_file.write(head1+"\n")
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output_vcf_file.write(head2+"\n")
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output_vcf_file.write(head3+"\n")
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def getProportionNonref(list):
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total_bases = int(list[total_depth_index]) - int(list[rev_i_index].split(":")[1]) - int(list[rev_d_index].split(":")[1]) - int(list[for_i_index].split(":")[1]) - int(list[for_d_index].split(":")[1])
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ref_base = list[ref_offset]
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if ( ref_base == "A" ):
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ref_bases = int(list[for_a_index].split(":")[1]) + int(list[rev_a_index].split(":")[1])
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elif ( ref_base == "C"):
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ref_bases = int(list[for_c_index].split(":")[1]) + int(list[rev_c_index].split(":")[1])
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elif ( ref_base == "G"):
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ref_bases = int(list[for_g_index].split(":")[1]) + int(list[rev_g_index].split(":")[1])
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else:
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ref_bases = int(list[for_t_index].split(":")[1]) + int(list[rev_t_index].split(":")[1])
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return 1.0 - ( float(ref_bases) / float(total_bases) )
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def generateVCFLine(chrom, pos, db, ref, alt, filt, qual, INFO):
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# make the info into a single string
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infoString = ""
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for keval in INFO:
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info = "=".join(keval)
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infoString = infoString+info
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format = "GT:GQ"
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genotype = "0/1:"+qual
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all_fields = [chrom, pos, db, ref, alt, qual, filt, infoString, format, genotype]
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return "\t".join(all_fields)
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# instantiate a line buffer
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two_lines_ago = [];
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previous_line = [];
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this_line = [];
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next_line = [];
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line_after_next = [];
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# read through the file
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for line in raw_calls_file.readlines():
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spline = line.strip().split()
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# iterate through the lines
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two_lines_ago = previous_line
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previous_line = this_line
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this_line = next_line
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next_line = line_after_next
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line_after_next = spline
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# window has been updated
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if ( not this_line ):
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continue # window not filled yet
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else:
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if ( float(this_line[lod_score_index]) > 0 and this_line[call_index] != "D" and this_line[call_index] != "I"):
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# potential call
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chrom = this_line[chrompos].split(":")[0]
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pos = this_line[chrompos].split(":")[1]
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ref = this_line[ref_offset]
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alt = this_line[call_index]
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lod = this_line[lod_score_index]
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# standard vcf info made -- now add INFO
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# syzy depth
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syz_depth = this_line[total_depth_index]
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# syzy strand bias
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syz_sb = ""
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if ( this_line[fish_flag] == "NA" ):
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syz_sb = "-1"
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else:
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syz_sb = this_line[fish_pval_index]
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# syzy neighborhood mismatch rate
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next_mmr = getProportionNonref(next_line)
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after_next_mmr = getProportionNonref(line_after_next)
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prev_mmr = getProportionNonref(previous_line)
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before_last_mmr = getProportionNonref(two_lines_ago)
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syzy_nmmr = str(next_mmr+after_next_mmr+prev_mmr+before_last_mmr)
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# turn these into key value pairs
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INFO = [["syzy_DP",syz_depth],[";syzy_SB",syz_sb],[";syzy_NMMR",syzy_nmmr]] # semicolons are a complete hack
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# get the vcf line
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vcfLine = generateVCFLine(chrom, pos, dbsnp, ref, alt, filter, lod, INFO)
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# print the sucker
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output_vcf_file.write(vcfLine+"\n")
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