Mercurial > repos > iuc > medaka_variant_pipeline
changeset 5:efca385ce679 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3"
| author | iuc |
|---|---|
| date | Fri, 16 Oct 2020 17:05:01 +0000 |
| parents | 5c959a2dde5f |
| children | ea1833858055 |
| files | annotateVCF.py |
| diffstat | 1 files changed, 15 insertions(+), 4 deletions(-) [+] |
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--- a/annotateVCF.py Tue Oct 13 15:59:54 2020 +0000 +++ b/annotateVCF.py Fri Oct 16 17:05:01 2020 +0000 @@ -75,6 +75,7 @@ ins_str += base else: ins_len = int(ins_str) - 1 + ins_str = "" insertion = base ins_flag = False elif del_flag: @@ -82,6 +83,7 @@ del_str += base else: del_len = int(del_str) - 1 + del_str = "" deletion = base del_flag = False else: @@ -107,7 +109,10 @@ else: counts[base_to_idx[base]] += 1 stranded_counts[base_to_idx_stranded[base]] += 1 - af = float(counts[base_to_idx[alt_base]]) / float(sum(counts)) + if sum(counts) == 0: + af = float("nan") + else: + af = float(counts[base_to_idx[alt_base]]) / float(sum(counts)) if float(sum(stranded_counts[0:4])) == 0: faf = float("nan") else: @@ -293,7 +298,10 @@ else: counts[8] += 1 dp = int(fields[3]) - af = float(counts[3]) / float(sum([counts[0], counts[3], counts[6]])) + if sum([counts[0], counts[3], counts[6]]) == 0: + af = float("nan") + else: + af = float(counts[3]) / float(sum([counts[0], counts[3], counts[6]])) if sum([counts[1], counts[4], counts[7]]) == 0: faf = float("nan") else: @@ -317,7 +325,7 @@ if line[0:2] == "##": out_vcf.write(line) elif line[0] == "#": - out_vcf.write("##annotateVCFVersion=0.1\n") + out_vcf.write("##annotateVCFVersion=0.2\n") out_vcf.write("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw Depth\">\n") out_vcf.write("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">\n") out_vcf.write("##INFO=<ID=FAF,Number=1,Type=Float,Description=\"Forward Allele Frequency\">\n") @@ -376,7 +384,10 @@ else: info = fields[7].split(';') info.append("DP=%d" % (dp)) - info.append("AF=%.6f" % (af)) + if isnan(af): + info.append("AF=NaN") + else: + info.append("AF=%.6f" % (af)) if isnan(faf): info.append("FAF=NaN") else: