augur.translate module¶
Translate gene regions from nucleotides to amino acids.
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exception
augur.translate.
MismatchNodeError
¶ Bases:
Exception
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exception
augur.translate.
MissingNodeError
¶ Bases:
Exception
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augur.translate.
assign_aa_fasta
(tree, translations)¶
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augur.translate.
assign_aa_vcf
(tree, translations)¶
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augur.translate.
construct_mut
(start, pos, end)¶
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augur.translate.
get_genes_from_file
(fname)¶
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augur.translate.
register_arguments
(parser)¶
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augur.translate.
run
(args)¶
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augur.translate.
safe_translate
(sequence, report_exceptions=False)¶ Returns an amino acid translation of the given nucleotide sequence accounting for gaps in the given sequence.
Optionally, returns a tuple of the translated sequence and whether an exception was raised during initial translation.
>>> safe_translate("ATG") 'M' >>> safe_translate("ATGGT-") 'MX' >>> safe_translate("ATG---") 'M-' >>> safe_translate("ATGTAG") 'M*' >>> safe_translate("") '' >>> safe_translate("ATGT") 'MX' >>> safe_translate("ATG", report_exceptions=True) ('M', False) >>> safe_translate("ATGA-G", report_exceptions=True) ('MX', True)
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augur.translate.
translate_feature
(aln, feature)¶ Translates a subsequence of input nucleotide sequences.
- Parameters
aln (dict) – sequences indexed by node name
feature (Bio.Seq.Seq) – BioPython sequence feature
- Returns
translated sequences indexed by node name
- Return type
dict
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augur.translate.
translate_vcf_feature
(sequences, ref, feature)¶ Translates a subsequence of input nucleotide sequences.
- Parameters
sequences (dict) – TreeTime format dictionary from VCF-input of sequences indexed by node name
ref – reference alignment the VCF was mapped to
feature (Bio.Seq.Seq) – BioPython sequence feature
- Returns
translated reference gene, positions of AA differences, and AA differences indexed by node name
- Return type
dict