On this Biopython tutorial, they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module:
from Bio import AlignIO
alignment = AlignIO.read(open("alignment.xmfa"), "mauve")
but I get the following error:
ValueError
Traceback (most recent call last) <ipython-input-30-396e54791d7a> in <module>()
----> 1 alignment = AlignIO.read(open("/Users/cr517/Documents/alignment.xmfa"),
"mauve")
/Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
in read(handle, format, seq_count, alphabet)
422 iterator = parse(handle, format, seq_count, alphabet)
423 try:
--> 424 first = next(iterator)
425 except StopIteration:
426 first = None
/Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
in parse(handle, format, seq_count, alphabet)
366 seq_count=seq_count)
367 else:
--> 368 raise ValueError("Unknown format '%s'" % format)
369
370 # This imposes some overhead... wait until we drop Python 2.4 to fix it
ValueError: Unknown format 'mauve'
