Bio.codonalign package
Submodules
Module contents
Code for dealing with Codon Alignments.
- Bio.codonalign.build(pro_align, nucl_seqs, corr_dict=None, gap_char='-', unknown='X', codon_table=None, complete_protein=False, anchor_len=10, max_score=10)
Build a codon alignment from protein alignment and corresponding nucleotides.
- Arguments:
pro_align - a protein MultipleSeqAlignment object
nucl_seqs - an object returned by SeqIO.parse or SeqIO.index or a collection of SeqRecord.
corr_dict - a dict that maps protein id to nucleotide id
complete_protein - whether the sequence begins with a start codon
Return a CodonAlignment object.
The example below answers this Biostars question: https://www.biostars.org/p/89741/
>>> from Bio.Seq import Seq >>> from Bio.SeqRecord import SeqRecord >>> from Bio.Align import MultipleSeqAlignment >>> from Bio.codonalign import build >>> seq1 = SeqRecord(Seq('ATGTCTCGT'), id='pro1') >>> seq2 = SeqRecord(Seq('ATGCGT'), id='pro2') >>> pro1 = SeqRecord(Seq('MSR'), id='pro1') >>> pro2 = SeqRecord(Seq('M-R'), id='pro2') >>> aln = MultipleSeqAlignment([pro1, pro2]) >>> codon_aln = build(aln, [seq1, seq2]) >>> print(codon_aln) CodonAlignment with 2 rows and 9 columns (3 codons) ATGTCTCGT pro1 ATG---CGT pro2