Manual Reference Pages - BIO::ALIGNIO::MSF (3)
Bio::AlignIO::msf - msf sequence input/output stream
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from msf
flat file databases.
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
AUTHORS - Peter Schattner
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
Returns : Bio::Align::AlignI object
Args : NONE
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
|perl v5.20.3 ||BIO::ALIGNIO::MSF (3) ||2016-04-05 |
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