Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
# do not use the object directly
use Bio::AlignIO;
# read in an alignment from the EMBOSS program water
my $in = new Bio::AlignIO(-format => 'emboss',
-file => 'seq.water');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.
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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.
Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
or on error
Args : NONE
Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in emboss format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object
