Bio::AlignIO nexus
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Summary
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
Package variables
No package variables defined.
Inherit
Bio::AlignIO
Synopsis
Do not use this module directly. Use it via the Bio::AlignIO class.
    use Bio::AlignIO;
my $in = Bio::AlignIO->new(-format => 'nexus', -file => 'aln.nexus'); while( my $aln = $in->next_aln ) { # do something with the alignment }
Description
This object can transform Bio::Align::AlignI objects to and from NEXUS
data blocks. See method documentation for supported NEXUS features.
Methods
BEGIN Code
_initialize
No description
Code
next_alnDescriptionCode
_read_taxlabels
No description
Code
write_alnDescriptionCode
flagDescriptionCode
Methods description
next_alncode    nextTop
 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 : Bio::Align::AlignI object
Args :
write_alncodeprevnextTop
 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 : Bio::Align::AlignI object
flagcodeprevnextTop
 Title   : flag
Usage : $obj->flag($name,$value)
Function: Get/Set a flag value
Returns : value of flag (a scalar)
Args : on set, new value (a scalar or undef, optional)
Methods code
BEGINTop
BEGIN {
    %valid_type = map {$_, 1} qw( dna rna protein standard );
    # standard throws error: inherited from Bio::PrimarySeq
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);
    my ($show_symbols, $endblock) = 
	$self->_rearrange([qw(SHOW_SYMBOLS SHOW_ENDBLOCK)], @args);
    my @names = qw(symbols endblock);
    for my $v ( $show_symbols, $endblock ) {
	$v = 1 unless defined $v; # default value is 1
my $n = shift @names; $self->flag($n, $v); }
}
next_alndescriptionprevnextTop
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);
    local $Bio::LocatableSeq::OTHER_SYMBOLS = '\*\?\.';
    local $Bio::LocatableSeq::GAP_SYMBOLS = '\-';
    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 defined $entry && $entry =~ /^\s+$/; return unless $entry; $self->throw("Not a valid interleaved NEXUS file! [#NEXUS] not starting the file\n$entry") unless ($entry && $entry =~ /^#NEXUS/i); # skip anything before either the taxa or data block
# but read in the optional title in a comment
while (defined($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 $incomment; while (defined ($entry = $self->_readline)) { local ($_) = $entry; next if s/\[[^\]]+\]//g; # remove comments
if( s/\[[^\]]+$// ) { $incomment = 1; # skip line if it is now empty or contains only whitespace
next if /^\s*$/; } elsif($incomment) { if( s/^[^\]]*\]// ) { $incomment = 0; } else { next; } } elsif( /taxlabels/i ) { # doesn't deal with taxlabels adequately and can mess things up!
# @names = $self->_read_taxlabels;
} else { /ntax\s*=\s*(\d+)/i and $seqcount = $1; /nchar\s*=\s*(\d+)/i and $residuecount = $1; /matchchar\s*=\s*(.)/i and $match = $1; /gap\s*=\s*(.)/i and $gap = $1; /missing\s*=\s*(.)/i and $missing = $1; /equate\s*=\s*\"([^\"]+)/i and $equate = $1; # "e.g. equate="T=C G=A";
/datatype\s*=\s*(\w+)/i and $alphabet = lc $1; /interleave/i and $interleave = 1 ; last if /matrix/io; } } $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}; $self->throw("\"$gap\" is not a valid gap character. For compatability, gap char can not be one of: ()[]{}/\,;:=*'`\"<>^") if $gap && $gap =~ /[\(\)\[\]\{\}\/\\\,\;\:\=\*\'\`\<\>\^]/; $self->throw("\"$missing\" is not a valid missing character. For compatability, missing char can not be one of: ()[]{}/\,;:=*'`\"<>^") if $missing && $missing =~ /[\(\)\[\]\{\}\/\\\,\;\:\=\*\'\`\<\>\^]/; $aln->gap_char($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; if( s/\[[^\]]+\]//g ) { #] remove comments
next if /^\s*$/; # skip line if it is now empty or contains only whitespace
} if ($interleave && defined$count && ($count <= $seqcount)) { /^\s+$/ and last; } else { /^\s+$/ and next; } /^\s*;/ and last; # stop if colon at end of matrix is on it's own line
#/^\s*;\s*$/ and last;
if ( /^\s*([\"\'](.+?)[\"\']|(\S+))\s+(.*)\s*$/ ) { # get single and double quoted names, or all the first
# nonwhite word as the name, and remained is seq
#if (/^\s*('([^']*?)'|([^']\S*))\s+(.*)$/) { #'
$name = ($2 || $3); if ($4) { # seq is on same line as name
# this is the usual NEXUS format
$str = $4; } else { # otherwise get seq from following lines. No comments allowed
# a less common matrix format, usually used for very long seqs
$str=''; while (local ($_) = $self->_readline) { my $str_tmp = $_; $str_tmp =~ s/[\s;]//g; $str .= $str_tmp; last if length$str == $residuecount; } } $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; /;/ and last; # stop if colon at end of matrix is on the same line as the last seq
} } # interleaved sections
$count = 0; if ( $interleave ) { # only read next section if file is interleaved
while( $entry = $self->_readline) { local ($_) = $entry; if( s/\[[^\]]+\]//g ) { #] remove comments
next if /^\s*$/; # skip line if it is now empty or contains only whitespace
} /^\s*;/ and last; # stop if colon at end of matrix is on it's own line
$count = 0, next if $entry =~ /^\s*$/; if (/^\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; /;/ and last; # stop if colon at end of matrix is on the same line as the last seq
} } return 0 if @names < 1; # sequence creation
$count = 0; foreach $name ( @names ) { $count++; if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) { ($seqname,$start,$end) = ($1,$2,$3); } else { ($seqname,$start,$str) = ($name,1,$hash{$count}); $str =~ s/[$Bio::LocatableSeq::GAP_SYMBOLS]//g; $end = length($str); } # consistency test
$self->throw("Length of sequence [$seqname] is not [$residuecount]; got".CORE::length($hash{$count})) unless CORE::length($hash{$count}) == $residuecount; $seq = Bio::LocatableSeq->new('-seq' => $hash{$count}, '-display_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 (defined $entry && $entry !~ /endblock/i) { $entry = $self->_readline; } return $aln if $aln->num_sequences; return;
}
_read_taxlabelsdescriptionprevnextTop
sub _read_taxlabels {
    my ($self) = @_;
    my ($name, @names);
    while (my $entry = $self->_readline) {
	last if $entry =~ m/^\s*(END)?;/i;
if( $entry =~ m/\s*(\S+)\s+/ ) {
(
$name) = ($1);
$name =~ s/\[[^\[]+\]//g; $name =~ s/\W/_/g; push @names, $name; } } return @names;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($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->num_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( $self->flag('symbols') && $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));

                     # account for single quotes round names
my $indent = $aln->maxdisplayname_length+2; $aln->set_displayname_flat(); foreach $seq ( $aln->each_seq() ) { my $nmid = $aln->displayname($seq->get_nse()); if( $nmid =~ /[^\w\d\.]/ ) { # put name in single quotes incase it contains any of
# the following chars: ()[]{}/\,;:=*'"`+-<> that are not
# allowed in PAUP* and possible other software
$name = sprintf("%-${indent}s", "\'" . $nmid . "\'"); } else { $name = sprintf("%-${indent}s", $nmid); } $hash{$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; } if( $self->flag('endblock') ) { $self->_print (";\n\nendblock;\n"); } else { $self->_print (";\n\nend;\n"); } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1;
}
flagdescriptionprevnextTop
sub flag {
    my ($self,$name,$val) = @_;
    return $self->{'flag'}->{$name} = $val if defined $val;
    return $self->{'flag'}->{$name};
}

1;
}
General documentation
ACKNOWLEDGEMENTSTop
Will Fisher has written an excellent standalone NEXUS format parser in
Perl, readnexus. A number of tricks were adapted from it.
FEEDBACKTop
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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename');
Function: returns a new Bio::AlignIO object to handle clustalw files
Returns : Bio::AlignIO::clustalw object
Args : -verbose => verbosity setting (-1,0,1,2)
-file => name of file to read in or with ">" - writeout
-fh => alternative to -file param - provide a filehandle
to read from/write to
-format => type of Alignment Format to process or produce
Customization of nexus flavor output -show_symbols => print the symbols="ATGC" in the data definition (MrBayes does not like this) boolean [default is 1] -show_endblock => print an 'endblock;' at the end of the data (MyBayes does not like this) boolean [default is 1]