Raw content of Bio::AlignIO::nexus
<![CDATA[# $Id: nexus.pm,v 1.12.2.1 2003/04/07 15:17:17 heikki Exp $
#
# BioPerl module for Bio::AlignIO::nexus
#
# Copyright Heikki Lehvaslaiho
#
=head1 NAME
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform L<Bio::Align::AlignI> objects to and from NEXUS
data blocks. See method documentation for supported NEXUS features.
=head1 ACKNOWLEDGEMENTS
Will Fisher has written an excellent standalone NEXUS format parser in
perl, readnexus. A number of tricks were adapted from it.
=head1 FEEDBACK
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHORS - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
=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...
package Bio::AlignIO::nexus;
use vars qw(@ISA %valid_type);
use strict;
no strict "refs";
use Bio::AlignIO;
@ISA = qw(Bio::AlignIO);
BEGIN {
%valid_type = 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 NEXUS format features:
- The file has to start with '#NEXUS'
- Reads in the name of the alignment from a comment
(anything after 'TITLE: ') .
- Sequence names can be given in a taxa block, too.
- If matchchar notation is used, converts
them back to sequence characters.
- Does character conversions specified in the
NEXUS equate command.
- Sequence names of type 'Homo sapiens' and
Homo_sapiens are treated identically.
Returns : L<Bio::Align::AlignI> object
Args :
=cut
sub next_aln {
my $self = shift;
my $entry;
my ($aln_name, $seqcount, $residuecount, %hash, $alphabet,
$match, $gap, $missing, $equate, $interleave,
$name,$str,@names,$seqname,$start,$end,$count,$seq);
my $aln = Bio::SimpleAlign->new(-source => 'nexus');
# file starts with '#NEXUS' but we allow white space only lines before it
$entry = $self->_readline;
$entry = $self->_readline while $entry =~ /^\s+$/;
return unless $entry;
$self->throw("Not a valid interleaved NEXUS file! [#NEXUS] not starting the file\n$entry")
unless $entry =~ /^#NEXUS/i;
# skip anything before either the taxa or data block
# but read in the optional title in a comment
while (defined($entry = $self->_readline)) {
local ($_) = $entry;
/\[TITLE. *([^\]]+)]\s+/i and $aln_name = $1;
last if /^begin +data/i || /^begin +taxa/i;
}
$aln_name =~ s/\s/_/g and $aln->id($aln_name) if $aln_name;
# data and taxa blocks
my $taxlabels;
while ($entry = $self->_readline) {
local ($_) = $entry;
# read in seq names if in taxa block
$taxlabels = 1 if /taxlabels/i;
if ($taxlabels) {
@names = $self->_read_taxlabels;
$taxlabels = 0;
}
/ntax ?= ?(\d+)/i and $seqcount = $1;
/nchar ?= ?(\d+)/i and $residuecount = $1;
/matchchar ?= ?(.)/i and $match = $1;
/gap ?= ?(.)/i and $gap = $1;
/missing ?= ?(.)/i and $missing = $1;
/equate ?= ?"([^\"]+)/i and $equate = $1; # "e.g. equate="T=C G=A";
/datatype ?= ?(\w+)/i and $alphabet = lc $1;
/interleave/i and $interleave = 1 ;
last if /matrix/i;
}
$self->throw("Not a valid NEXUS sequence file. Datatype not specified")
unless $alphabet;
$self->throw("Not a valid NEXUS sequence file. Datatype should not be [$alphabet]")
unless $valid_type{$alphabet};
$aln->gap_char($gap);
$aln->missing_char($missing);
#
# if data is not right after the matrix line
# read the empty lines out
#
while ($entry = $self->_readline) {
unless ($entry =~ /^\s+$/) {
$self->_pushback($entry);
last;
}
}
#
# matrix command
#
# first alignment section
if (@names == 0) { # taxa block did not exist
while ($entry = $self->_readline) {
local ($_) = $entry;
s/\[[^[]+\]//g; #] remove comments
if ($interleave) {
/^\s+$/ and last;
} else {
/^\s+$/ and next;
}
/^\s*;\s*$/ and last;
if (/^\s*('([^']*?)'|([^']\S*))\s+(.*)\s$/) { #'
$name = ($2 || $3);
$str = $4;
$name =~ s/ /_/g;
push @names, $name;
$str =~ s/\s//g;
$count = @names;
$hash{$count} = $str;
};
$self->throw("Not a valid interleaved NEXUS file!
seqcount [$count] > predeclared [$seqcount] in the first section") if $count > $seqcount;
}
}
# interleaved sections
$count = 0;
while( $entry = $self->_readline) {
local ($_) = $entry;
s/\[[^[]+\]//g; #] remove comments
last if /^\s*;/;
$count = 0, next if $entry =~ /^\s*$/;
if (/^\s*('([^']*?)'|([^']\S*))\s+(.*)\s$/) { #'
$str = $4;
$str =~ s/\s//g;
$count++;
$hash{$count} .= $str;
};
$self->throw("Not a valid interleaved NEXUS file!
seqcount [$count] > predeclared [$seqcount] ") if $count > $seqcount;
}
return 0 if @names < 1;
# sequence creation
$count = 0;
foreach $name ( @names ) {
$count++;
if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname = $1;
$start = $2;
$end = $3;
} else {
$seqname=$name;
$start = 1;
$str = $hash{$count};
$str =~ s/[^A-Za-z]//g;
$end = length($str);
}
# consistency test
$self->throw("Length of sequence [$seqname] is not [$residuecount]! ")
unless CORE::length($hash{$count}) == $residuecount;
$seq = new Bio::LocatableSeq('-seq'=>$hash{$count},
'-id'=>$seqname,
'-start'=>$start,
'-end'=>$end,
'alphabet'=>$alphabet
);
$aln->add_seq($seq);
}
# if matchchar is used
$aln->unmatch($match) if $match;
# if equate ( e.g. equate="T=C G=A") is used
if ($equate) {
$aln->map_chars($1, $2) while $equate =~ /(\S)=(\S)/g;
}
while ($entry !~ /endblock/i) {
$entry = $self->_readline;
}
return $aln;
}
sub _read_taxlabels {
my ($self) = @_;
my ($name, @names);
while (my $entry = $self->_readline) {
($name) = $entry =~ /\s*(\S+)\s+/;
$name =~ s/\[[^\[]+\]//g;
$name =~ s/\W/_/g;
push @names, $name;
last if /^\s*;/;
}
return @names;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: Writes the $aln object into the stream in interleaved NEXUS
format. Everything is written into a data block.
SimpleAlign methods match_char, missing_char and gap_char must be set
if you want to see them in the output.
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
my $count = 0;
my $wrapped = 0;
my $maxname;
my ($length,$date,$name,$seq,$miss,$pad,%hash,@arr,$tempcount,$index );
my ($match, $missing, $gap,$symbols) = ('', '', '','');
foreach my $aln (@aln) {
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
$self->throw("All sequences in the alignment must be the same length")
unless $aln->is_flush($self->verbose);
$length = $aln->length();
$self->_print (sprintf("#NEXUS\n[TITLE: %s]\n\nbegin data;\ndimensions ntax=%s nchar=%s;\n",
$aln->id, $aln->no_sequences, $length));
$match = "match=". $aln->match_char if $aln->match_char;
$missing = "missing=". $aln->missing_char if $aln->missing_char;
$gap = "gap=". $aln->gap_char if $aln->gap_char;
$symbols = 'symbols="'.join('',$aln->symbol_chars). '"' if( $aln->symbol_chars);
$self->_print (sprintf("format interleave datatype=%s %s %s %s %s;\n\nmatrix\n",
$aln->get_seq_by_pos(1)->alphabet, $match, $missing, $gap, $symbols));
my $indent = $aln->maxdisplayname_length;
$aln->set_displayname_flat();
foreach $seq ( $aln->each_seq() ) {
$name = $aln->displayname($seq->get_nse());
$name = sprintf("%-${indent}s", $name);
$hash{$name} = $seq->seq();
push(@arr,$name);
}
while( $count < $length ) {
# there is another block to go!
foreach $name ( @arr ) {
my $dispname = $name;
# $dispname = '' if $wrapped;
$self->_print (sprintf("%${indent}s ",$dispname));
$tempcount = $count;
$index = 0;
while( ($tempcount + 10 < $length) && ($index < 5) ) {
$self->_print (sprintf("%s ",substr($hash{$name},$tempcount,10)));
$tempcount += 10;
$index++;
}
# last
if( $index < 5) {
# space to print!
$self->_print (sprintf("%s ",substr($hash{$name},$tempcount)));
$tempcount += 10;
}
$self->_print ("\n");
}
$self->_print ("\n\n");
$count = $tempcount;
$wrapped = 1;
}
$self->_print (";\n\nendblock;\n");
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
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