#
# BioPerl module for FAST::Bio::AlignIO::proda
#
# based on the FAST::Bio::SeqIO modules
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
# and the FAST::Bio::SimpleAlign module of Ewan Birney
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::AlignIO::proda - proda sequence input/output stream
This provides the basic capabilities to parse the output alignments
from the ProDA multiple sequence alignment program
=head1 SYNOPSIS
Do not use this module directly. Use it via the FAST::Bio::AlignIO class.
=head1 DESCRIPTION
This object can transform FAST::Bio::Align::AlignI objects to and from proda
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:
=head1 AUTHORS - Albert Vilella
Email: avilella-at-gmail-dot-com
=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($LINELENGTH);
use strict;
$LINELENGTH = 60;
=head2 new
Title : new
Usage : $alignio = FAST::Bio::AlignIO->new(-format => 'proda',
-file => 'filename');
Function: returns a new FAST::Bio::AlignIO object to handle proda files
Returns : FAST::Bio::AlignIO::proda 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 (proda 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 = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : FAST::Bio::Align::AlignI object
Args : NONE
See L<FAST::Bio::Align::AlignI> for details
=cut
sub next_aln {
my ($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 !~ /\(/ )
{
$self->throw(
"trying to parse a file which does not start with proda headers"
);
} else {
# use it inside the loop
$self->_pushback($first_line);
}
my %alignments;
my $aln = FAST::Bio::SimpleAlign->new(
-source => 'proda',
-verbose => $self->verbose
);
my $order = 0;
my %order;
$self->{_lastline} = '';
my ($first_block, $seen_block, $seen_header) = (0,0,0);
my @ids; my @ids_copy;
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 proda header
if (/\(/ && $seen_header) {
$self->_pushback($_);
last;
}
if (/\(/ && !$seen_header) {
@ids = split(' ', $_);
$seen_header = 1;
next;
}
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} = $_;
next;
}
# we ended up the first block and now are on the second
@ids_copy = @ids unless(defined($ids_copy[0])); #FIXME - hacky
my $seqname_with_coords = shift(@ids_copy);
if ($seqname_with_coords !~ /$seqname/) {
{
$self->throw("header and body of the alignment dont match");
}
}
$alignments{$seqname_with_coords} .= $aln_line;
if ( !$seen_block ) {
if (exists $order{$seqname_with_coords}) {
$self->warn("Duplicate sequence : $seqname\n".
"Can't guarantee alignment quality");
}
else {
$order{$seqname_with_coords} = $order++;
}
}
}
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 = FAST::Bio::LocatableSeq->new(
-seq => $alignments{$name},
-id => $sname,
-start => $start,
-end => $end,
-alphabet => $self->alphabet,
);
$aln->add_seq($seq);
}
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the proda-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : FAST::Bio::Align::AlignI object
=cut
sub write_aln {
my ($self,@aln) = @_;
$self->throw_not_implemented();
}
=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'};
}
=head2 no_header
Title : no_header
Usage : $obj->no_header($newval)
Function: Set if the alignment input has a CLUSTAL header or not
Returns : value of no_header
Args : newvalue (optional)
=cut
sub no_header {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'_no_header'} = $value;
}
return $self->{'_no_header'};
}
1;