Mercurial > repos > jjohnson > ensembl_variant_report
comparison ensembl_variant_report.py @ 8:fd612f8119a2 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit f003aece24587f68b883449f278f1e601110e2ec-dirty
| author | jjohnson |
|---|---|
| date | Tue, 17 Jul 2018 12:21:36 -0400 |
| parents | d5cb252c68da |
| children | 0ef485da6ba6 |
comparison
equal
deleted
inserted
replaced
| 7:d5cb252c68da | 8:fd612f8119a2 |
|---|---|
| 94 ref = fields[ri] | 94 ref = fields[ri] |
| 95 alts = fields[ai] | 95 alts = fields[ai] |
| 96 dp = int(fields[di]) | 96 dp = int(fields[di]) |
| 97 dpr = [int(x) for x in fields[fi].split(',')] | 97 dpr = [int(x) for x in fields[fi].split(',')] |
| 98 for i,alt in enumerate(alts.split(',')): | 98 for i,alt in enumerate(alts.split(',')): |
| 99 freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None | 99 freq = float(dpr[i+1])/float(dp) if dp and dpr else \ |
| 100 float(dpr[i+1])/float(sum(dpr)) if dpr else None | |
| 100 yield (transcript,pos,ref,alt,dp,freq) | 101 yield (transcript,pos,ref,alt,dp,freq) |
| 101 | 102 |
| 102 def parse_snpeff_vcf(): | 103 def parse_snpeff_vcf(): |
| 103 for linenum,line in enumerate(inputFile): | 104 for linenum,line in enumerate(inputFile): |
| 104 if line.startswith('##'): | 105 if line.startswith('##'): |
| 129 (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|') | 130 (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|') |
| 130 elif key == 'EFF': | 131 elif key == 'EFF': |
| 131 (eff, effs) = effect.rstrip(')').split('(') | 132 (eff, effs) = effect.rstrip(')').split('(') |
| 132 (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11] | 133 (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11] |
| 133 i = alt_list.index(alt) if alt in alt_list else 0 | 134 i = alt_list.index(alt) if alt in alt_list else 0 |
| 134 freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None | 135 freq = float(dpr[i+1])/float(dp) if dp and dpr else \ |
| 136 float(dpr[i+1])/float(sum(dpr)) if dpr else None | |
| 135 yield (transcript,pos,ref,alt,dp,freq) | 137 yield (transcript,pos,ref,alt,dp,freq) |
| 136 | 138 |
| 137 | 139 |
| 138 #Process gene model | 140 #Process gene model |
| 139 ens_ref = None | 141 ens_ref = None |