Mercurial > repos > jjohnson > snpeff_cds_report
comparison snpEff_cds_report.py @ 7:fbb6510186df default tip
when codon has ambiguous nucleotide translate to X
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 15 Sep 2014 06:13:47 -0500 |
| parents | a64ef0611117 |
| children |
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| 6:a64ef0611117 | 7:fbb6510186df |
|---|---|
| 35 | 35 |
| 36 def translate(seq) : | 36 def translate(seq) : |
| 37 rna = seq.upper().replace('T','U') | 37 rna = seq.upper().replace('T','U') |
| 38 aa = [] | 38 aa = [] |
| 39 for i in range(0,len(rna) - 2, 3): | 39 for i in range(0,len(rna) - 2, 3): |
| 40 aa.append(codon_map[rna[i:i+3]]) | 40 codon = rna[i:i+3] |
| 41 aa.append(codon_map[codon] if codon in codon_map else 'X') | |
| 41 return ''.join(aa) | 42 return ''.join(aa) |
| 42 | 43 |
| 43 """ | 44 """ |
| 44 SNfEffect vcf reported variations to the reference sequence, so need to reverse complement for coding sequences on the negative strand | 45 SNfEffect vcf reported variations to the reference sequence, so need to reverse complement for coding sequences on the negative strand |
| 45 Queries that request a sequence always return the sequence in the first column regardless of the order of attributes. | 46 Queries that request a sequence always return the sequence in the first column regardless of the order of attributes. |