Bio::AlignIO emboss
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Summary
Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Inherit
Bio::AlignIO
Synopsis
    # do not use the object directly
use Bio::AlignIO;
# read in an alignment from the EMBOSS program water
my $in = Bio::AlignIO->new(-format => 'emboss',
-file => 'seq.water');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
Description
This object handles parsing and writing pairwise sequence alignments
from the EMBOSS suite.
Methods
BEGIN Code
_initialize
No description
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.
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 emboss format
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
Methods code
BEGINTop
BEGIN {
    $EMBOSSTitleLen    = 13;
    $EMBOSSLineLen     = 50;
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    $self->{'_type'} = undef;
}
next_alndescriptionprevnextTop
sub next_aln {
    my ($self) = @_;
    my $seenbegin = 0;
    my %data = ( 'seq1' => {
		     'start'=> undef,
		     'end'=> undef,
		     'name' => '',
		     'data' => '' },
		 'seq2' => {
		     'start'=> undef,
		     'end'=> undef,
		     'name' => '',
		     'data' => '' },
		 'align' => '',
		 'type'  => $self->{'_type'},  # to restore type from
# previous aln if possible
); my %names; while( defined($_ = $self->_readline) ) { next if( /^\#?\s+$/ || /^\#+\s*$/ ); if( /^\#(\=|\-)+\s*$/) { last if( $seenbegin); } elsif( /(Local|Global):\s*(\S+)\s+vs\s+(\S+)/ || /^\#\s+Program:\s+(\S+)/ ) { my ($name1,$name2) = ($2,$3); if( ! defined $name1 ) { # Handle EMBOSS 2.2.X
$data{'type'} = $1; $name1 = $name2 = ''; } else { $data{'type'} = $1 eq 'Local' ? 'water' : 'needle'; } $data{'seq1'}->{'name'} = $name1; $data{'seq2'}->{'name'} = $name2; $self->{'_type'} = $data{'type'}; } elsif( /Score:\s+(\S+)/ ) { $data{'score'} = $1; } elsif( /^\#\s+(1|2):\s+(\S+)/ && ! $data{"seq$1"}->{'name'} ) { my $nm = $2; $nm = substr($nm,0,$EMBOSSTitleLen); # emboss has a max seq length
if( $names{$nm} ) { $nm .= "-". $names{$nm}; } $names{$nm}++; $data{"seq$1"}->{'name'} = $nm; } elsif( $data{'seq1'}->{'name'} && /^\Q$data{'seq1'}->{'name'}/ ) { my $count = 0; $seenbegin = 1; my @current; while( defined ($_) ) { my $align_other = ''; my $delayed; if($count == 0 || $count == 2 ) { my @l = split; my ($seq,$align,$start,$end); if( $count == 2 && $data{'seq2'}->{'name'} eq '' ) { # weird boundary condition
($start,$align,$end) = @l; } elsif( @l == 3 ) { $align = ''; ($seq,$start,$end) = @l } else { ($seq,$start,$align,$end) = @l; } my $seqname = sprintf("seq%d", ($count == 0) ? '1' : '2'); $data{$seqname}->{'data'} .= $align; $data{$seqname}->{'start'} ||= $start; $data{$seqname}->{'end'} = $end; $current[$count] = [ $start,$align || '']; } else { s/^\s+//; s/\s+$//; $data{'align'} .= $_; } BOTTOM: last if( $count++ == 2); $_ = $self->_readline(); } if( $data{'type'} eq 'needle' ) { # which ever one is shorter we want to bring it up to
# length. Man this stinks.
my ($s1,$s2) = ($data{'seq1'}, $data{'seq2'}); my $d = length($current[0]->[1]) - length($current[2]->[1]); if( $d < 0 ) { # s1 is smaller, need to add some
# compare the starting points for this alignment line
if( $current[0]->[0] <= 1 ) { $s1->{'data'} = ('-' x abs($d)) . $s1->{'data'}; $data{'align'} = (' 'x abs($d)).$data{'align'}; } else { $s1->{'data'} .= '-' x abs($d); $data{'align'} .= ' 'x abs($d); } } elsif( $d > 0) { # s2 is smaller, need to add some
if( $current[2]->[0] <= 1 ) { $s2->{'data'} = ('-' x abs($d)) . $s2->{'data'}; $data{'align'} = (' 'x abs($d)).$data{'align'}; } else { $s2->{'data'} .= '-' x abs($d); $data{'align'} .= ' 'x abs($d); } } } } } return unless $seenbegin; my $aln = Bio::SimpleAlign->new(-verbose => $self->verbose(), -score => $data{'score'}, -source => "EMBOSS-".$data{'type'}); foreach my $seqname ( qw(seq1 seq2) ) { return unless ( defined $data{$seqname} ); $data{$seqname}->{'name'} ||= $seqname; my $seq = Bio::LocatableSeq->new ('-seq' => $data{$seqname}->{'data'}, '-display_id' => $data{$seqname}->{'name'}, '-start' => $data{$seqname}->{'start'}, '-end' => $data{$seqname}->{'end'}, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } return $aln;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;

    $self->throw("Sorry: writing emboss output is not currently available!\n ");
}

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 via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _