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forgot to commit this earlier 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2264 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2009-12-04 22:10:16 +00:00
parent 4c147329a9
commit 0f89a38473
1 changed files with 16 additions and 13 deletions
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29
python/SyzygyCallsFileToVCF.py
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@ -112,7 +112,7 @@ for line in raw_calls_file.readlines():
# window has been updated
if ( not this_line ):
if ( not two_lines_ago ):
continue # window not filled yet
else:
if ( float(this_line[lod_score_index]) > 0 and this_line[call_index] != "D" and this_line[call_index] != "I"):
@ -132,15 +132,18 @@ for line in raw_calls_file.readlines():
syz_sb = "-1"
else:
syz_sb = this_line[fish_pval_index]
# syzy neighborhood mismatch rate
next_mmr = getProportionNonref(next_line)
after_next_mmr = getProportionNonref(line_after_next)
prev_mmr = getProportionNonref(previous_line)
before_last_mmr = getProportionNonref(two_lines_ago)
syzy_nmmr = str(next_mmr+after_next_mmr+prev_mmr+before_last_mmr)
# turn these into key value pairs
INFO = [["syzy_DP",syz_depth],[";syzy_SB",syz_sb],[";syzy_NMMR",syzy_nmmr]] # semicolons are a complete hack
# get the vcf line
vcfLine = generateVCFLine(chrom, pos, dbsnp, ref, alt, filter, lod, INFO)
# print the sucker
output_vcf_file.write(vcfLine+"\n")
# do we want any other kind of annotations here ??
# syzy neighborhood mismatch rate
next_mmr = getProportionNonref(next_line) # from later in genome
after_next_mmr = getProportionNonref(line_after_next) # from same
prev_mmr = getProportionNonref(previous_line) # from earlier
before_last_mmr = getProportionNonref(two_lines_ago) # same
syzy_nmmr = str(next_mmr+after_next_mmr+prev_mmr+before_last_mmr)
# turn these into key value pairs
INFO = [["syzy_DP",syz_depth],[";syzy_SB",syz_sb],[";syzy_NMMR",syzy_nmmr]] # semicolons are a complete hack
# get the vcf line
vcfLine = generateVCFLine(chrom, pos, dbsnp, ref, alt, filter, lod, INFO)
# print the sucker
output_vcf_file.write(vcfLine+"\n")