#
# BioPerl module for Bio::AlignIO::clustalw
#
# based on the Bio::SeqIO modules
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
# and the Bio::SimpleAlign module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# History
# September 5, 2000
# POD documentation - main docs before the code
=head1 NAME
Bio::AlignIO::clustalw - clustalw sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
=head1 DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from clustalw
files.
=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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
=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::clustalw;
use vars qw($LINELENGTH $CLUSTALPRINTVERSION);
use strict;
$LINELENGTH = 60;
$CLUSTALPRINTVERSION = '1.81';
use base qw(Bio::AlignIO);
=head2 new
Title : new
Usage : $alignio = Bio::AlignIO->new(-format => 'clustalw',
-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 to write, with ">"
-fh => alternative to -file param - provide a filehandle
to read from or write to
-format => alignment format to process or produce
-percentages => display a percentage of identity
in each line of the alignment (clustalw only)
-linelength=> alignment output line length (default 60)
=cut
sub _initialize {
my ( $self, @args ) = @_;
$self->SUPER::_initialize(@args);
my ( $percentages, $ll ) =
$self->_rearrange( [qw(PERCENTAGES LINELENGTH)], @args );
defined $percentages && $self->percentages($percentages);
$self->line_length( $ll || $LINELENGTH );
}
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args : NONE
See L<Bio::Align::AlignI> for details
=cut
sub next_aln {
my ($self) = @_;
my $first_line;
while ( $first_line = $self->_readline ) {
last if $first_line !~ /^$/;
}
$self->_pushback($first_line);
if ( defined( $first_line = $self->_readline )
&& $first_line !~ /CLUSTAL/ )
{
$self->throw(
"trying to parse a file which does not start with a CLUSTAL header"
);
}
my %alignments;
my $aln = Bio::SimpleAlign->new(
-source => 'clustalw',
-verbose => $self->verbose
);
my $order = 0;
my %order;
$self->{_lastline} = '';
my ($first_block, $seen_block) = (0,0);
while ( defined( $_ = $self->_readline ) ) {
next if (/^\s+$/ && !$first_block);
if (/^\s$/) { # line contains no description
$seen_block = 1;
next;
}
$first_block = 1;
# break the loop if we come to the end of the current alignment
# and push back the CLUSTAL header
if (/CLUSTAL/) {
$self->_pushback($_);
last;
}
my ( $seqname, $aln_line ) = ( '', '' );
if (/^\s*(\S+)\s*\/\s*(\d+)-(\d+)\s+(\S+)\s*$/ox) {
# clustal 1.4 format
( $seqname, $aln_line ) = ( "$1:$2-$3", $4 );
# } elsif( /^\s*(\S+)\s+(\S+)\s*$/ox ) { without trailing numbers
}
elsif (/^\s*(\S+)\s+(\S+)\s*\d*\s*$/ox) { # with numbers
( $seqname, $aln_line ) = ( $1, $2 );
if ( $seqname =~ /^[\*\.\+\:]+$/ ) {
$self->{_lastline} = $_;
next;
}
}
else {
$self->{_lastline} = $_;
next;
}
if ( !$seen_block ) {
if (exists $order{$seqname}) {
$self->warn("Duplicate sequence : $seqname\n".
"Can't guarantee alignment quality");
}
else {
$order{$seqname} = $order++;
}
}
$alignments{$seqname} .= $aln_line;
}
my ( $sname, $start, $end );
foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments ) {
if ( $name =~ /(\S+):(\d+)-(\d+)/ ) {
( $sname, $start, $end ) = ( $1, $2, $3 );
}
else {
( $sname, $start ) = ( $name, 1 );
my $str = $alignments{$name};
$str =~ s/[^A-Za-z]//g;
$end = length($str);
}
my $seq = Bio::LocatableSeq->new
(
'-seq' => $alignments{$name},
'-display_id' => $sname,
'-start' => $start,
'-end' => $end,
'-alphabet' => $self->alphabet,
);
$aln->add_seq($seq);
}
# not sure if this should be a default option - or we can pass in
# an option to do this in the future? --jason stajich
# $aln->map_chars('\.','-');
# no sequences added, so just return
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the clustalw-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
=cut
sub write_aln {
my ( $self, @aln ) = @_;
my ( $count, $length, $seq, @seq, $tempcount, $line_len );
$line_len = $self->line_length || $LINELENGTH;
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;
}
my $matchline = $aln->match_line;
if ( $self->force_displayname_flat ) {
$aln->set_displayname_flat(1);
}
$self->_print(
sprintf( "CLUSTAL W (%s) multiple sequence alignment\n\n\n",
$CLUSTALPRINTVERSION )
) or return;
$length = $aln->length();
$count = $tempcount = 0;
@seq = $aln->each_seq();
my $max = 22;
foreach $seq (@seq) {
$max = length( $aln->displayname( $seq->get_nse() ) )
if ( length( $aln->displayname( $seq->get_nse() ) ) > $max );
}
while ( $count < $length ) {
my ( $linesubstr, $first ) = ( '', 1 );
foreach $seq (@seq) {
#
# Following lines are to suppress warnings
# if some sequences in the alignment are much longer than others.
my ($substring);
my $seqchars = $seq->seq();
SWITCH: {
if ( length($seqchars) >= ( $count + $line_len ) ) {
$substring = substr( $seqchars, $count, $line_len );
if ($first) {
$linesubstr =
substr( $matchline, $count, $line_len );
$first = 0;
}
last SWITCH;
}
elsif ( length($seqchars) >= $count ) {
$substring = substr( $seqchars, $count );
if ($first) {
$linesubstr = substr( $matchline, $count );
$first = 0;
}
last SWITCH;
}
$substring = "";
}
$self->_print(
sprintf(
"%-" . $max . "s %s\n",
$aln->displayname( $seq->get_nse() ), $substring
)
) or return;
}
my $percentages = '';
if ( $self->percentages ) {
my ($strcpy) = ($linesubstr);
my $count = ( $strcpy =~ tr/\*// );
$percentages =
sprintf( "\t%d%%", 100 * ( $count / length($linesubstr) ) );
}
$self->_print(
sprintf(
"%-" . $max . "s %s%s\n",
'', $linesubstr, $percentages
)
);
$self->_print( sprintf("\n\n") ) or return;
$count += $line_len;
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 percentages
Title : percentages
Usage : $obj->percentages($newval)
Function: Set the percentages flag - whether or not to show percentages in
each output line
Returns : value of percentages
Args : newvalue (optional)
=cut
sub percentages {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_percentages'} = $value;
}
return $self->{'_percentages'};
}
=head2 line_length
Title : line_length
Usage : $obj->line_length($newval)
Function: Set the alignment output line length
Returns : value of line_length
Args : newvalue (optional)
=cut
sub line_length {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_line_length'} = $value;
}
return $self->{'_line_length'};
}
1;