Bio::AlignIO::msf(3pm) User Contributed Perl Documentation Bio::AlignIO::msf(3pm)
NAME
Bio::AlignIO::msf - msf sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from msf flat file databases.
FEEDBACK
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
Reporting Bugs
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
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
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
$aln->map_chars('~','-')
Returns : Bio::Align::AlignI object
Args : NONE
write_aln
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 v5.14.2 2012-03-02 Bio::AlignIO::msf(3pm)