Bio::AlignIO mega
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Summary
Bio::AlignIO::mega - Parse and Create MEGA format data files
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Bio::SimpleAlign
Inherit
Bio::AlignIO
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).
Methods
BEGIN Code
next_alnDescriptionCode
write_alnDescriptionCode
Methods description
next_alncode    nextTop
 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 : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : NONE
write_alncodeprevnextTop
 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 : Bio::Align::AlignI object
Methods code
BEGINTop
BEGIN {
  $MEGANAMELEN = 10;
  $LINELEN = 60;
  $BLOCKLEN = 10;
  %VALID_TYPES =  map {$_, 1} qw( dna rna protein standard);
}
next_alndescriptionprevnextTop
sub next_aln {
   my ($self) = @_;
   my $entry;
   my ($alphabet,%seqs);
   local $Bio::LocatableSeq::OTHER_SYMBOLS = '\*\?\.';
   local $Bio::LocatableSeq::GAP_SYMBOLS = '\-';
   my $aln = 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}; $s =~ s/[$Bio::LocatableSeq::GAP_SYMBOLS]+//g; my $end = length($s); my $seq = Bio::LocatableSeq->new('-alphabet' => $alphabet, '-display_id' => $seqname, '-seq' => $seqs{$seqname}, '-start' => 1, '-end' => $end); $aln->add_seq($seq); } $aln->unmatch; return $aln if $aln->num_sequences; return;
}
write_alndescriptionprevnextTop
sub write_aln {
   my ($self,@aln) = @_;
   my $count = 0;
   my $wrapped = 0;
   my $maxname;

   foreach my $aln ( @aln ) {
       if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) {
	   $self->warn("Must provide a 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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _