NAME
FAST::Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the FAST::Bio::AlignIO class.
DESCRIPTION
This object can transform FAST::Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the FAST::Bio::SearchIO module.
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
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.
Returns : FAST::Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<FAST::Bio::Align::AlignI> object_get_len
Title : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence stringwidth
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)