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.
-
__next__
(self)¶ Parse the next alignment from the handle.
-