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 = Bio::AlignIO->new(-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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.