Mercurial > repos > peterjc > align_back_trans
diff tools/align_back_trans/align_back_trans.py @ 4:c8469274d136 draft
v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package
author | peterjc |
---|---|
date | Wed, 10 May 2017 12:05:28 -0400 |
parents | de803005027f |
children | 2c32e8a8990f |
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--- a/tools/align_back_trans/align_back_trans.py Wed Feb 01 06:55:27 2017 -0500 +++ b/tools/align_back_trans/align_back_trans.py Wed May 10 12:05:28 2017 -0400 @@ -18,12 +18,14 @@ """ import sys -from Bio.Seq import Seq -from Bio.Alphabet import generic_protein + +from Bio import AlignIO +from Bio import SeqIO + from Bio.Align import MultipleSeqAlignment -from Bio import SeqIO -from Bio import AlignIO +from Bio.Alphabet import generic_protein from Bio.Data.CodonTable import ambiguous_generic_by_id +from Bio.Seq import Seq if "-v" in sys.argv or "--version" in sys.argv: print "v0.0.7" @@ -130,19 +132,23 @@ def alignment_back_translate(protein_alignment, nucleotide_records, key_function=None, gap=None, table=0): """Thread nucleotide sequences onto a protein alignment.""" # TODO - Separate arguments for protein and nucleotide gap characters? - if key_function is None: - key_function = lambda x: x if gap is None: gap = "-" aligned = [] - for protein in protein_alignment: - try: - nucleotide = nucleotide_records[key_function(protein.id)] - except KeyError: - raise ValueError("Could not find nucleotide sequence for protein %r" - % protein.id) - aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + try: + if key_function is None: + for protein in protein_alignment: + nucleotide = nucleotide_records[protein.id] + aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + else: + for protein in protein_alignment: + nucleotide = nucleotide_records[key_function(protein.id)] + aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + except KeyError: + raise ValueError("Could not find nucleotide sequence for protein %r" + % protein.id) + return MultipleSeqAlignment(aligned)