Minor changes (additional info calculated)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2522 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
parent
fdd14e1a01
commit
dfe160ff77
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@ -31,28 +31,31 @@ 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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try:
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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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except ValueError:
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print("ERROR: no index for a header field in call file. Initial line was")
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print(header)
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# now print the VCF header
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head1 = "##source=Syzygy"
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@ -64,6 +67,27 @@ 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 getProportionNonrefThatAreSNP(list):
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ref_base = list[ref_offset]
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a_bases = int(list[for_a_index].split(":")[1]) + int(list[rev_a_index].split(":")[1])
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c_bases = int(list[for_c_index].split(":")[1]) + int(list[rev_c_index].split(":")[1])
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g_bases = int(list[for_g_index].split(":")[1]) + int(list[rev_g_index].split(":")[1])
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t_bases = int(list[for_t_index].split(":")[1]) + int(list[rev_t_index].split(":")[1])
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if ( ref_base == "A" ):
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snp_base_counts = max(c_bases,g_bases,t_bases)
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nonref_counts = c_bases+g_bases+t_bases
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elif ( ref_base == "C"):
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snp_base_counts = max(a_bases,g_bases,t_bases)
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nonref_counts = a_bases+g_bases+t_bases
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elif ( ref_base == "G"):
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snp_base_counts = max(a_bases,c_bases,t_bases)
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nonref_counts = a_bases+c_bases+t_bases
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else:
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snp_base_counts = max(a_bases,c_bases,g_bases)
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nonref_counts = a_bases+c_bases+g_bases
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return ( float(snp_base_counts + 1)/float(nonref_counts+1) )
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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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@ -115,7 +139,17 @@ for line in raw_calls_file.readlines():
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if ( not two_lines_ago ):
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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]) > 1 and this_line[call_index] != "D" and this_line[call_index] != "I"):
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try:
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is_potential_call = float(this_line[lod_score_index]) > 1 and this_line[call_index] != "D" and this_line[call_index] != "I"
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except IndexError as err:
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print(this_line)
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print(lod_score_index)
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raise IndexError(str(err))
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except ValueError as err:
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print(this_line)
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print(lod_score_index)
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raise(ValueError(str(err)))
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if ( is_potential_call):
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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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@ -136,14 +170,15 @@ for line in raw_calls_file.readlines():
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# do we want any other kind of annotations here ??
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# syzy neighborhood mismatch rate
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pileup_noise = str(1.0-getProportionNonrefThatAreSNP(this_line))
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next_mmr = getProportionNonref(next_line) # from later in genome
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after_next_mmr = getProportionNonref(line_after_next) # from same
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prev_mmr = getProportionNonref(previous_line) # from earlier
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before_last_mmr = getProportionNonref(two_lines_ago) # same
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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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INFO = [["syzy_DP",syz_depth],[";syzy_SB",syz_sb],[";syzy_NMMR",syzy_nmmr],[";syzy_residMismatch",pileup_noise],[";syzy_originalLOD",lod]] # 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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vcfLine = generateVCFLine(chrom, pos, dbsnp, ref, alt, filter, str(float(lod)*10.0), INFO)
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# print the sucker
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output_vcf_file.write(vcfLine+"\n")
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