support translation of ambiguity codes #30
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this is linked to this hgvs package issue: biocommons/hgvs#595 |
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@reece we need a solution for this bug immediately, please review ASAP |
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Will look today. Thanks for the contribution. |
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Also, assuming this PR is good to merge, could you publish a new version of bioutils to pypi? Thanks! |
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Thanks for the contribution, Kaylee.
This implementation translates any code with an ambiguity code as X. However, it's often possible to translate codons with ambiguity codes where the ambiguity is irrelevant to the outcome. Since we're adding ambiguity support, I think we should strive for the fuller support eventually. I'll follow up on slack with discussion for some options on how to proceed.
src/bioutils/sequences.py
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| @@ -441,7 +453,12 @@ def translate_cds(seq, full_codons=True, ter_symbol="*"): | |||
| protein_seq = list() | |||
| for i in range(0, len(seq) - len(seq) % 3, 3): | |||
| try: | |||
| aa = dna_to_aa1_lut[seq[i:i + 3]] | |||
| the_seq = seq[i:i + 3] | |||
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Can we rename the_seq to codon for clarity?
src/bioutils/sequences.py
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| aa = dna_to_aa1_lut[seq[i:i + 3]] | ||
| the_seq = seq[i:i + 3] | ||
| wildcard_nucleotides = ["B", "D", "H", "V", "N", "U", "W", "S", "M", "K", "R", "Y", "Z"] | ||
| if any([wildcard_base in the_seq for wildcard_base in wildcard_nucleotides]): |
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As written, any wildcard cause the AA to be X. I think we can do better than that. For example, in a standard translation table, CUN ⇒ Leu, GCN ⇒ Ala, GGN ⇒ Gly, AAY ⇒ Asn, etc. See overall comments for discussion.
src/bioutils/sequences.py
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| @@ -441,7 +453,12 @@ def translate_cds(seq, full_codons=True, ter_symbol="*"): | |||
| protein_seq = list() | |||
| for i in range(0, len(seq) - len(seq) % 3, 3): | |||
| try: | |||
| aa = dna_to_aa1_lut[seq[i:i + 3]] | |||
| the_seq = seq[i:i + 3] | |||
| wildcard_nucleotides = ["B", "D", "H", "V", "N", "U", "W", "S", "M", "K", "R", "Y", "Z"] | |||
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IUPAC calls these "ambiguity codes". Please use that name so that the intent is clearer.
(e.g., something like iupac_ambiguity_codes = "BDHVNUWSMKRYZ")
Also, a list of chars is better written as a string for readability. (Lists and strings are both Sequences and have the same interface for lookup, length, iterability, etc.)
reece
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