Bio::Tools pSW
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Summary
Bio::Tools::pSW - pairwise Smith Waterman object
Package variables
No package variables defined.
Included modules
Bio::SimpleAlign
Inherit
Bio::Tools::AlignFactory
Synopsis
    use Bio::Tools::pSW;
use Bio::AlignIO;
my $factory = Bio::Tools::pSW->new( '-matrix' => 'blosum62.bla',
'-gap' => 12,
'-ext' => 2,
);
#use the factory to make some output $factory->align_and_show($seq1,$seq2,STDOUT); # make a Bio::SimpleAlign and do something with it my $aln = $factory->pairwise_alignment($seq1,$seq2); my $alnout = Bio::AlignIO->new(-format => 'msf', -fh => \*STDOUT); $alnout->write_aln($aln);
Description
pSW is an Alignment Factory for protein sequences. It builds pairwise
alignments using the Smith-Waterman algorithm. The alignment algorithm is
implemented in C and added in using an XS extension. The XS extension basically
comes from the Wise2 package, but has been slimmed down to only be the
alignment part of that (this is a good thing!). The XS extension comes
from the bioperl-ext package which is distributed along with bioperl.
Warning: This package will not work if you have not compiled the
bioperl-ext package.
The mixture of C and Perl is ideal for this sort of
problem. Here are some plus points for this strategy:
  Speed and Memory
  The algorithm is actually implemented in C, which means it is faster than
a pure perl implementation (I have never done one, so I have no idea
how faster) and will use considerably less memory, as it efficiently
assigns memory for the calculation.
  Algorithm efficiency
  The algorithm was written using Dynamite, and so contains an automatic
switch to the linear space divide-and-conquer method. This means you
could effectively align very large sequences without killing your machine
(it could take a while though!).
Methods
BEGIN Code
new
No description
Code
pairwise_alignmentDescriptionCode
align_and_showDescriptionCode
matrixDescriptionCode
gapDescriptionCode
extDescriptionCode
Methods description
pairwise_alignmentcode    nextTop
 Title   : pairwise_alignment
Usage : $aln = $factory->pairwise_alignment($seq1,$seq2)
Function: Makes a SimpleAlign object from two sequences
Returns : A SimpleAlign object
Args :
align_and_showcodeprevnextTop
 Title   : align_and_show
Usage : $factory->align_and_show($seq1,$seq2,STDOUT)
matrixcodeprevnextTop
 Title     : matrix()
Usage : $factory->matrix('blosum62.bla');
Function : Reads in comparison matrix based on name
:
Returns :
Argument : comparison matrix
gapcodeprevnextTop
 Title     : gap
Usage : $gap = $factory->gap() #get
: $factory->gap($value) #set
Function : the set get for the gap penalty
Example :
Returns : gap value
Arguments : new value
extcodeprevnextTop
 Title     : ext
Usage : $ext = $factory->ext() #get
: $factory->ext($value) #set
Function : the set get for the ext penalty
Example :
Returns : ext value
Arguments : new value
Methods code
BEGINTop
BEGIN {
    eval {
	require Bio::Ext::Align;
    };
    if ( $@ ) {
	die("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please read the install the bioperl-ext package\n\n");
	exit(1);
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  
  my $self = $class->SUPER::new(@args);

  my($matrix,$gap,$ext) = $self->_rearrange([qw(MATRIX
						GAP
						EXT
						)],@args);
  
  #default values - we have to load matrix into memory, so 
# we need to check it out now
if( ! defined $matrix || !($matrix =~ /\w/) ) { $matrix = 'blosum62.bla'; } $self->matrix($matrix); # will throw exception if it can't load it
$self->gap(12) unless defined $gap; $self->ext(2) unless defined $ext; # I'm pretty sure I am not doing this right... ho hum...
# This was not roght ($gap and $ext could not be 0) It is fixed now /AE
if( defined $gap ) { if( $gap =~ /^\d+$/ ) { $self->gap($gap); } else { $self->throw("Gap penalty must be a number, not [$gap]"); } } if( defined $ext ) { if( $ext =~ /^\d+$/ ) { $self->ext($ext); } else { $self->throw("Extension penalty must be a number, not [$ext]"); } } return $self;
}
pairwise_alignmentdescriptionprevnextTop
sub pairwise_alignment {
    my ($self,$seq1,$seq2) = @_;
    my($t1,$t2,$aln,$out,@str1,@str2,@ostr1,@ostr2,$alc,$tstr,$tid,$start1,$end1,$start2,$end2,$alctemp);
    
    if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') ||
	! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) {
	$self->warn("Cannot call pairwise_alignment without specifing 2 sequences (Bio::PrimarySeqI objects)");
	return;
    }
    # fix Jitterbug #1044
if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } $self->set_memory_and_report(); # create engine objects
$seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); $t1 = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(), $seq1->seq()); $t2 = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(), $seq2->seq()); $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext); if( ! defined $aln || $aln == 0 ) { $self->throw("Unable to build an alignment"); } # free sequence engine objects
$t1 = $t2 = 0; # now we have to get into the AlnBlock structure and
# figure out what is aligned to what...
# we are going to need the sequences as arrays for convience
@str1 = split(//, $seq1->seq()); @str2 = split(//, $seq2->seq()); # get out start points
# The alignment is in alignment coordinates - ie the first
# residues starts at -1 and ends at 0. (weird I know).
# bio-coordinates are +2 from this...
$start1 = $aln->start()->alu(0)->start +2; $start2 = $aln->start()->alu(1)->start +2; # step along the linked list of alc units...
for($alc = $aln->start();$alc->at_end() != 1;$alc = $alc->next()) { if( $alc->alu(0)->text_label eq 'SEQUENCE' ) { push(@ostr1,$str1[$alc->alu(0)->start+1]); } else { # assumme it is in insert!
push(@ostr1,'-'); } if( $alc->alu(1)->text_label eq 'SEQUENCE' ) { push(@ostr2,$str2[$alc->alu(1)->start+1]); } else { # assumme it is in insert!
push(@ostr2,'-'); } $alctemp = $alc; } #
# get out end points
#
# end points = real residue end in 'C' coordinates = residue
# end in biocoordinates. Oh... the wonder of coordinate systems!
$end1 = $alctemp->alu(0)->end+1; $end2 = $alctemp->alu(1)->end+1; # get rid of the alnblock
$alc = 0; $aln = 0; # new SimpleAlignment
$out = Bio::SimpleAlign->new(); # new SimpleAlignment
$tstr = join('',@ostr1); $tid = $seq1->id(); $out->add_seq(Bio::LocatableSeq->new( -seq=> $tstr, -start => $start1, -end => $end1, -id=>$tid )); $tstr = join('',@ostr2); $tid = $seq2->id(); $out->add_seq(Bio::LocatableSeq->new( -seq=> $tstr, -start => $start2, -end => $end2, -id=> $tid )); # give'm back the alignment
return $out;
}
align_and_showdescriptionprevnextTop
sub align_and_show {
    my($self,$seq1,$seq2,$fh) = @_;
    my($t1,$t2,$aln,$id,$str);

if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') ||
	! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) {
	$self->warn("Cannot call align_and_show without specifing 2 sequences (Bio::PrimarySeqI objects)");
	return;
    }
    # fix Jitterbug #1044
if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } if( ! defined $fh ) { $fh =\* STDOUT; } $self->set_memory_and_report(); $seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); $t1 = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->seq()); $t2 = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->seq()); $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext); if( ! defined $aln || $aln == 0 ) { $self->throw("Unable to build an alignment"); } &Bio::Ext::Align::write_pretty_seq_align($aln,$t1,$t2,12,50,$fh);
}
matrixdescriptionprevnextTop
sub matrix {
    my($self,$comp) = @_;
    my $temp;

    if( !defined $comp ) {
	$self->throw("You must have a comparison matrix to set!");
    }

    # talking to the engine here...
$temp = &Bio::Ext::Align::CompMat::read_Blast_file_CompMat($comp); if( !(defined $temp) || $temp == 0 ) { $self->throw("$comp cannot be read as a BLAST comparison matrix file"); } $self->{'matrix'} = $temp;
}
gapdescriptionprevnextTop
sub gap {
    my ($self,$val) = @_;
    

    if( defined $val ) {
	if( $val < 0 ) {    # Fixed so that gap==0 is allowed /AE
$self->throw("Can't have a gap penalty less than 0"); } $self->{'gap'} = $val; } return $self->{'gap'};
}
extdescriptionprevnextTop
sub ext {
    my ($self,$val) = @_;
    
    if( defined $val ) {
	if( $val < 0 ) {    # Fixed so that gap==0 is allowed /AE
$self->throw("Can't have a gap penalty less than 0"); } $self->{'ext'} = $val; } return $self->{'ext'}; } 1;
}
General documentation
INSTALLATIONTop
This module is included with the central Bioperl distribution:
   http://bio.perl.org/Core/Latest
ftp://bio.perl.org/pub/DIST
Follow the installation instructions included in the INSTALL file.
FEEDBACKTop
Mailing Lists Top
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
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/
AUTHORTop
Ewan Birney, birney-at-sanger.ac.uk or birney-at-ebi.ac.uk
CONTRIBUTORSTop
Jason Stajich, jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an underscore "_".