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 tool 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)
Bases:
AlignmentIterator
GCG MSF alignment iterator.
- __next__()
Parse the next alignment from the handle.