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://github.com/bioperl/bioperl-live/issues

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