#
# BioPerl module for FAST::Bio::AlignIO::mega
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::AlignIO::mega - Parse and Create MEGA format data files
=head1 SYNOPSIS
use FAST::Bio::AlignIO;
my $alignio = FAST::Bio::AlignIO->new(-format => 'mega',
-file => 't/data/hemoglobinA.meg');
while( my $aln = $alignio->next_aln ) {
# process each alignment or convert to another format like NEXUS
}
=head1 DESCRIPTION
This object handles reading and writing data streams in the MEGA
format (Kumar and Nei).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted the
web:
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
use vars qw($MEGANAMELEN %VALID_TYPES $LINELEN $BLOCKLEN);
use strict;
# symbols are changed due to MEGA's use of '.' for redundant sequences
BEGIN {
$MEGANAMELEN = 10;
$LINELEN = 60;
$BLOCKLEN = 10;
%VALID_TYPES = map {$_, 1} qw( dna rna protein standard);
}
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Supports the following MEGA format features:
- The file has to start with '#mega'
- Reads in the name of the alignment from a comment
(anything after '!TITLE: ') .
- Reads in the format parameters datatype
Returns : L<FAST::Bio::Align::AlignI> object - returns 0 on end of file
or on error
Args : NONE
=cut
sub next_aln{
my ($self) = @_;
my $entry;
my ($alphabet,%seqs);
local $FAST::Bio::LocatableSeq::OTHER_SYMBOLS = '\*\?\.';
local $FAST::Bio::LocatableSeq::GAP_SYMBOLS = '\-';
my $aln = FAST::Bio::SimpleAlign->new(-source => 'mega');
while( defined($entry = $self->_readline()) && ($entry =~ /^\s+$/) ) {}
$self->throw("Not a valid MEGA file! [#mega] not starting the file!")
unless $entry =~ /^#mega/i;
while( defined($entry = $self->_readline() ) ) {
local($_) = $entry;
if(/\!Title:\s*([^\;]+)\s*/i) { $aln->id($1)}
elsif( s/\!Format\s+([^\;]+)\s*/$1/ ) {
my (@fields) = split(/\s+/,$1);
foreach my $f ( @fields ) {
my ($name,$value) = split(/\=/,$f);
if( $name eq 'datatype' ) {
$alphabet = $value;
} elsif( $name eq 'identical' ) {
$aln->match_char($value);
} elsif( $name eq 'indel' ) {
$aln->gap_char($value);
}
}
} elsif( /^\#/ ) {
last;
}
}
my @order;
while( defined($entry) ) {
if( $entry !~ /^\s+$/ ) {
# this is to skip the leading '#'
my $seqname = substr($entry,1,$MEGANAMELEN-1);
$seqname =~ s/(\S+)\s+$/$1/g;
my $line = substr($entry,$MEGANAMELEN);
$line =~ s/\s+//g;
if( ! defined $seqs{$seqname} ) {push @order, $seqname; }
$seqs{$seqname} .= $line;
}
$entry = $self->_readline();
}
foreach my $seqname ( @order ) {
my $s = $seqs{$seqname};
$s =~ s/[$FAST::Bio::LocatableSeq::GAP_SYMBOLS]+//g;
my $end = length($s);
my $seq = FAST::Bio::LocatableSeq->new('-alphabet' => $alphabet,
'-display_id' => $seqname,
'-seq' => $seqs{$seqname},
'-start' => 1,
'-end' => $end);
$aln->add_seq($seq);
}
$aln->unmatch;
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MEGA format
Returns : 1 for success and 0 for error
Args : L<FAST::Bio::Align::AlignI> object
=cut
sub write_aln{
my ($self,@aln) = @_;
my $count = 0;
my $wrapped = 0;
my $maxname;
foreach my $aln ( @aln ) {
if( ! $aln || ! $aln->isa('FAST::Bio::Align::AlignI') ) {
$self->warn("Must provide a FAST::Bio::Align::AlignI object when calling write_aln");
return 0;
} elsif( ! $aln->is_flush($self->verbose) ) {
$self->warn("All Sequences in the alignment must be the same length");
return 0;
}
$aln->match();
my $len = $aln->length();
my $format = sprintf('datatype=%s identical=%s indel=%s;',
$aln->get_seq_by_pos(1)->alphabet(),
$aln->match_char, $aln->gap_char);
$self->_print(sprintf("#mega\n!Title: %s;\n!Format %s\n\n\n",
$aln->id, $format));
my ($count, $blockcount,$length) = ( 0,0,$aln->length());
$aln->set_displayname_flat();
while( $count < $length ) {
foreach my $seq ( $aln->each_seq ) {
my $seqchars = $seq->seq();
$blockcount = 0;
my $substring = substr($seqchars, $count, $LINELEN);
my @blocks;
while( $blockcount < length($substring) ) {
push @blocks, substr($substring, $blockcount,$BLOCKLEN);
$blockcount += $BLOCKLEN;
}
$self->_print(sprintf("#%-".($MEGANAMELEN-1)."s%s\n",
substr($aln->displayname($seq->get_nse()),
0,$MEGANAMELEN-2),
join(' ', @blocks)));
}
$self->_print("\n");
$count += $LINELEN;
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;