skbio.format.sequences.fasta_from_alignment

skbio.format.sequences.fasta_from_alignment(aln, make_seqlabel=None, line_wrap=None, sort=True)[source]

Returns a FASTA string given an alignment object

Parameters:

aln : Alignment, dict

alignment or dictionary where the keys are the sequence ids and the values are the sequences themselves.

make_seqlabel : function, optional

callback function that takes the seq object and returns a label str. If None is passed, the following attributes will try to be retrieved in this order and the first to exist will be used: id, Label or Name. In any other case an integer with the position of the sequence object will be used.

line_wrap : int, optional

line_wrap: a integer for maximum line width, if None is passed the full sequence will be used.

sort : bool, optional

Whether or not the sequences should be sorted by their sequence id, default value is True.

Returns:

str

FASTA formatted string composed of the objects passed in via seqs.

Examples

Formatting a sequence alignment object into a FASTA file. >>> from skbio.core.alignment import Alignment >>> from skbio.core.sequence import DNA >>> from skbio.format.sequences import fasta_from_alignment >>> seqs = [DNA(“ACC–G-GGTA..”, id=”seq1”), ... DNA(“TCC–G-GGCA..”, id=”seqs2”)] >>> a1 = Alignment(seqs) >>> print fasta_from_alignment(a1) >seq1 ACC–G-GGTA.. >seqs2 TCC–G-GGCA..