Code for dealing with Codon Alignment.
CodonAlignment class is inherited from MultipleSeqAlignment class. This is the core class to deal with codon alignment in biopython.
- class Bio.codonalign.codonalignment.CodonAlignment(records='', name=None)¶
Codon Alignment class that inherits from MultipleSeqAlignment.
>>> from Bio.SeqRecord import SeqRecord >>> a = SeqRecord(CodonSeq("AAAACGTCG"), id="Alpha") >>> b = SeqRecord(CodonSeq("AAA---TCG"), id="Beta") >>> c = SeqRecord(CodonSeq("AAAAGGTGG"), id="Gamma") >>> print(CodonAlignment([a, b, c])) CodonAlignment with 3 rows and 9 columns (3 codons) AAAACGTCG Alpha AAA---TCG Beta AAAAGGTGG Gamma
- __init__(self, records='', name=None)¶
Initialize the class.
Return a multi-line string summary of the alignment.
This output is indicated to be readable, but large alignment is shown truncated. A maximum of 20 rows (sequences) and 60 columns (20 codons) are shown, with the record identifiers. This should fit nicely on a single screen. e.g.
- __getitem__(self, index)¶
Return a CodonAlignment object for single indexing.
- __add__(self, other)¶
Combine two codonalignments with the same number of rows by adding them.
The method also allows to combine a CodonAlignment object with a MultipleSeqAlignment object. The following rules apply:
CodonAlignment + CodonAlignment -> CodonAlignment
CodonAlignment + MultipleSeqAlignment -> MultipleSeqAlignment
Get alignment length.
Convert the CodonAlignment to a MultipleSeqAlignment.
Return a MultipleSeqAlignment containing all the SeqRecord in the CodonAlignment using Seq to store sequences
- get_dn_ds_matrix(self, method='NG86', codon_table=None)¶
Available methods include NG86, LWL85, YN00 and ML.
method - Available methods include NG86, LWL85, YN00 and ML.
codon_table - Codon table to use for forward translation.
- get_dn_ds_tree(self, dn_ds_method='NG86', tree_method='UPGMA', codon_table=None)¶
Construct dn tree and ds tree.
dn_ds_method - Available methods include NG86, LWL85, YN00 and ML.
tree_method - Available methods include UPGMA and NJ.
- classmethod from_msa(align)¶
Convert a MultipleSeqAlignment to CodonAlignment.
Function to convert a MultipleSeqAlignment to CodonAlignment. It is the user’s responsibility to ensure all the requirement needed by CodonAlignment is met.
- Bio.codonalign.codonalignment.mktest(codon_alns, codon_table=None, alpha=0.05)¶
McDonald-Kreitman test for neutrality.
Implement the McDonald-Kreitman test for neutrality (PMID: 1904993) This method counts changes rather than sites (http://mkt.uab.es/mkt/help_mkt.asp).
codon_alns - list of CodonAlignment to compare (each CodonAlignment object corresponds to gene sampled from a species)
Return the p-value of test result.