Mercurial > repos > jjohnson > ensembl_variant_report
diff ensembl_variant_report.py @ 3:652d35c42bca draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit d3b7ff1c2f0a1eed7a65af7208e987a35627402c-dirty
| author | jjohnson |
|---|---|
| date | Wed, 20 Mar 2019 15:27:02 -0400 |
| parents | f87fe6bc48f4 |
| children |
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--- a/ensembl_variant_report.py Mon Mar 18 21:43:34 2019 -0400 +++ b/ensembl_variant_report.py Wed Mar 20 15:27:02 2019 -0400 @@ -116,6 +116,7 @@ qual = float(qual) dp = None dpr = None + ao = None af = None for info_item in info.split(';'): if info_item.find('=') < 0: continue @@ -124,6 +125,8 @@ dp = int(val) if key == 'DPR' or key == 'AD': dpr = [int(x) for x in val.split(',')] + if key == 'AO': + ao = [int(x) for x in val.split(',')] if key == 'AF': af = [float(x) for x in val.split(',')] if key in ['EFF','ANN']: @@ -135,11 +138,14 @@ (eff, effs) = effect.rstrip(')').split('(') (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11] i = alt_list.index(alt) if alt in alt_list else 0 - if af: - freq = af[i] + if ao: + freq = float(ao[i])/float(dp) if dp else \ + float(dpr[i])/float(sum(ao)) elif dpr: freq = float(dpr[i+1])/float(dp) if dp else \ float(dpr[i+1])/float(sum(dpr)) + elif af: + freq = af[i] else: freq = None if freq: