Bio.AlignIO.MauveIO module

Bio.AlignIO support for “xmfa” output from Mauve/ProgressiveMauve.

You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences).

For example, consider a progressiveMauve alignment file containing the following:

#FormatVersion Mauve1
#Sequence1File      a.fa
#Sequence1Entry     1
#Sequence1Format    FastA
#Sequence2File      b.fa
#Sequence2Entry     2
#Sequence2Format    FastA
#Sequence3File      c.fa
#Sequence3Entry     3
#Sequence3Format    FastA
#BackboneFile       three.xmfa.bbcols
> 1:0-0 + a.fa
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
> 2:5417-5968 + b.fa
TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACGTGAGAGGAGCGCCCTAAGCTTTGGGAAATTCAAGC-
--------------------------------------------------------------------------------
CTGGAACGTACTTGCTGGTTTCGCTACTATTTCAAACAAGTTAGAGGCCGTTACCTCGGGCGAACGTATAAACCATTCTG
> 3:9476-10076 - c.fa
TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-GGGAGGAGATCGCCCCAAACGTATGGTGAGTCGGGCG
TTTCCTATAGCTATAGGACCAATCCACTTACCATACGCCCGGCGTCGCCCAGTCCGGTTCGGTACCCTCCATGACCCACG
---------------------------------------------------------AAATGAGGGCCCAGGGTATGCTT
=
> 2:5969-6015 + b.fa
-----------------------
GGGCGAACGTATAAACCATTCTG
> 3:9429-9476 - c.fa
TTCGGTACCCTCCATGACCCACG
AAATGAGGGCCCAGGGTATGCTT

This is a multiple sequence alignment with multiple aligned sections, so you would probably load this using the Bio.AlignIO.parse() function:

>>> from Bio import AlignIO
>>> align = AlignIO.parse("Mauve/simple_short.xmfa", "mauve")
>>> alignments = list(align)
>>> for aln in alignments:
...     print(aln)
...
Alignment with 3 rows and 240 columns
--------------------------------------------...--- a.fa
TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG b.fa/5416-5968
TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT c.fa/9475-10076
Alignment with 2 rows and 46 columns
-----------------------GGGCGAACGTATAAACCATTCTG b.fa/5968-6015
TTCGGTACCCTCCATGACCCACGAAATGAGGGCCCAGGGTATGCTT c.fa/9428-9476

Additional information is extracted from the XMFA file and available through the annotation attribute of each record:

>>> for record in alignments[0]:
...     print(record.id, len(record))
...     print("  start: %d, end: %d, strand: %d" %(
...         record.annotations['start'], record.annotations['end'],
...         record.annotations['strand']))
...
a.fa 240
  start: 0, end: 0, strand: 1
b.fa/5416-5968 240
  start: 5416, end: 5968, strand: 1
c.fa/9475-10076 240
  start: 9475, end: 10076, strand: -1

class Bio.AlignIO.MauveIO.MauveWriter(*args, **kwargs)

Bases: Bio.AlignIO.Interfaces.SequentialAlignmentWriter

Mauve/XMFA alignment writer.

__init__(*args, **kwargs)

Initialize the class.

write_alignment(alignment)

Use this to write (another) single alignment to an open file.

Note that sequences and their annotation are recorded together (rather than having a block of annotation followed by a block of aligned sequences).

class Bio.AlignIO.MauveIO.MauveIterator(handle, seq_count=None)

Bases: Bio.AlignIO.Interfaces.AlignmentIterator

Mauve xmfa alignment iterator.

__next__()

Parse the next alignment from the handle.