Bio::AlignIO::mega - Parse and Create MEGA format data files
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'mega',
-file => 't/data/hemoglobinA.meg');
while( my $aln = $alignio->next_aln ) {
# process each alignment or convert to another format like NEXUS
}
This object handles reading and writing data streams in the MEGA format (Kumar
and Nei).
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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.
Supports the following MEGA format features:
- The file has to start with '#mega'
- Reads in the name of the alignment from a comment
(anything after '!TITLE: ') .
- Reads in the format parameters datatype
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 MEGA format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object