sourCEntral - mobile manpages

pdf

Bio::AlignIO::mega

NAME

Bio::AlignIO::mega - Parse and Create MEGA format data files

SYNOPSIS

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
}

DESCRIPTION

This object handles reading and writing data streams in the MEGA format (Kumar and Nei).

FEEDBACK

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l AT bioperl DOT org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

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 of the bugs and their resolution. Bug reports can be submitted the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

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.
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

write_aln
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

pdf