Bio.AlignIO.MsfIO module

Bio.AlignIO support for GCG MSF format.

The file format was produced by the GCG PileUp and and LocalPileUp tools, and later tools such as T-COFFEE and MUSCLE support it as an optional output format.

The original GCG toola would write gaps at ends of each sequence which could be missing data as tildes (~), whereas internal gaps were periods (.) instead. This parser replaces both with minus signs (-) for consistency with the rest of Bio.AlignIO.

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).

class Bio.AlignIO.MsfIO.MsfIterator(handle, seq_count=None, alphabet=SingleLetterAlphabet())

Bases: Bio.AlignIO.Interfaces.AlignmentIterator

GCG MSF alignment iterator.


Parse the next alignment from the handle.