Bio::AlignIO::fasta

NAME

Bio::AlignIO::fasta - fasta MSA Sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from fasta flat files. 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 Bio::SearchIO module.

FEEDBACK

Support
Please direct usage questions or support issues to the mailing list:

bioperl-l AT bioperl DOT 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

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 : 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)

See Bio::Align::AlignI

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<Bio::Align::AlignI> object