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::

> 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.xmfa", "mauve")
     >>> alignments = list(align)
     >>> for aln in alignments:
     ...     print(align)
     SingleLetterAlphabet() alignment with 3 rows and 240 columns
     --------------------------------------------...--- 1
     TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG 2
     TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT 3
     SingleLetterAlphabet() alignment with 3 rows and 46 columns
     ---------------------------------------------- 1
     -----------------------GGGCGAACGTATAAACCATTCTG 2
     TTCGGTACCCTCCATGACCCACGAAATGAGGGCCCAGGGTATGCTT 3

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), record.annotations
     1 240 {'start': 0, 'end': 0, 'strand': 1}
     2 240 {'start': 5417, 'end': 5968, 'strand': 1}
     3 240 {'start': 9476, 'end': 10076, 'strand': -1}