Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

400 lines (312 sloc) 10.642 kB
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using
promoterwise
=head1 SYNOPSIS
# Build a Promoterwise alignment factory
my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
my $factory = Bio::Tools::Run::Promoterwise->new(@params);
my (@fp)= $factory->run($seq1,$seq2);
# each feature pair is a group of hsps
foreach my $fp(@fp){
print "Hit Length: ".$fp->feature1->length."\n";
print "Hit Start: ".$fp->feature1->start."\n";
print "Hit End: ".$fp->feature1->end."\n";
print "Hsps: \n";
my @first_hsp = $fp->feature1->sub_SeqFeature;
my @second_hsp = $fp->feature2->sub_SeqFeature;
for ($i..$#first_hsp){
print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
}
}
print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";
#Available parameters include:
#( S T U V QUERY_START QUERY_END TARGET_START
#TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
#LHREJECT LHMAX DYMEM KBYTE DYCACHE)
#For an explanation of these parameters, please see documentation
#from the Wise package.
=head1 DESCRIPTION
Promoterwise is an alignment algorithm that relaxes the constraint
that local alignments have to be co-linear. Otherwise it provides a
similar model to DBA, which is designed for promoter sequence
alignments by Ewan Birney. It is part of the wise2 package available
at: http://www.sanger.ac.uk/software/wise2.
=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:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email: shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Promoterwise;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@PROMOTERWISE_SWITCHES @PROMOTERWISE_PARAMS
@OTHER_SWITCHES %OK_FIELD);
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Promoterwise;
use strict;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase );
# Two ways to run the program .....
# 1. define an environmental variable WISEDIR
# export WISEDIR =/usr/local/share/wise2.2.0
# where the wise2.2.20 package is installed
#
# 2. include a definition of an environmental variable WISEDIR in
# every script that will use DBA.pm
# $ENV{WISEDIR} = '/usr/local/share/wise2.2.20';
BEGIN {
@PROMOTERWISE_PARAMS = qw( S T U V QUERY_START QUERY_END TARGET_START
TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
LHREJECT LHMAX DYMEM KBYTE DYCACHE);
@OTHER_SWITCHES = qw(SILENT QUIET ERROROFFSTD);
# Authorize attribute fields
foreach my $attr ( @PROMOTERWISE_PARAMS, @PROMOTERWISE_SWITCHES,
@OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'promoterwise';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{WISEDIR},"/src/bin/") if $ENV{WISEDIR};
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
return undef unless $self->executable;
my $prog = $self->executable;
my $string = `$prog -version`;
$string =~ /(Version *)/i;
return $1 || undef;
}
=head2 run
Title : run
Usage : 2 sequence objects
@fp = $factory->run($seq1, $seq2);
Function: run
Returns : An array of <Bio::SeqFeature::FeaturePair>
Args : Name of a file containing a set of 2 fasta sequences
or else 2 Bio::Seq objects.
Throws an exception if argument is not either a string (eg a filename)
or 2 Bio::Seq objects. If arguments are strings, throws exception if
file corresponding to string name can not be found.
=cut
sub run{
my ($self, $seq1, $seq2)=@_;
my ($attr, $value, $switch);
$self->io->_io_cleanup();
# Create input file pointer
my ($infile1,$infile2)= $self->_setinput($seq1, $seq2);
if (!($infile1 && $infile2))
{$self->throw("Bad input data (sequences need an id ) ");}
# run promoterwise
my @fp = $self->_run($infile1,$infile2);
return @fp;
}
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to a promoterwise program
Example :
Returns : L<Bio::SeqFeature::FeaturePair>
Args : Name of a files containing 2 sequences in the order of peptide and genomic
=cut
sub _run {
my ($self,$infile1,$infile2) = @_;
my $instring;
$self->debug( "Program ".$self->executable."\n");
unless ( $self->executable ) {
$self->throw("Cannot run Promoterwise unless the executable is found.".
" Check your environment variables or make sure ".
"promoterwise is in your path.");
}
my $paramstring = $self->_setparams;
my $commandstring = $self->executable." $infile1 $infile2 $paramstring";
# this is to capture STDERR messages which leak out when you run programs
# with open(FH, "... |");
if( ( $self->silent && $self->quiet) &&
($^O !~ /os2|dos|MSWin32|amigaos/) ) {
# yeah, like promoterwise is really going to run on Windows...
$commandstring .= ' -quiet -silent -erroroffstd 2> /dev/null';
}
$self->debug( "promoterwise command = $commandstring");
open(PW, "$commandstring |") ||
$self->throw( "Promoterwise call ($commandstring) crashed: $? \n");
my $pw_parser = Bio::Tools::Promoterwise->new(-fh=>\*PW,
-query1_seq=>$self->_query1_seq,
-query2_seq=>$self->_query2_seq);
my @fp;
while (my $fp = $pw_parser->next_result){
push @fp,$fp;
}
return @fp;
}
sub _setinput {
my ($self, $seq1, $seq2) = @_;
my ($tfh1,$tfh2,$outfile1,$outfile2);
$self->throw("calling with not enough arguments") unless $seq1 && $seq2;
# Not going to set _query_pep/_subject_dna_seq
# if you pass in a filename
unless( ref($seq1) ) {
unless( -e $seq1 ) {
$self->throw("Sequence1 is not a Bio::PrimarySeqI object nor file\n");
}
$outfile1 = $seq1;
}
else {
($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
my $out1 = Bio::SeqIO->new('-fh' => $tfh1,
'-format' => 'fasta');
$out1->write_seq($seq1);
$self->_query1_seq($seq1);
# Make sure you close things - this is what creates
# Out of filehandle errors
close($tfh1);
undef $tfh1;
}
unless( ref($seq2) ) {
unless( -e $seq2 ) {
$self->throw("Sequence2 is not a Bio::PrimarySeqI object nor file\n");
}
$outfile2 = $seq2;
}
else {
($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
my $out2 = Bio::SeqIO->new('-fh' => $tfh2,
'-format' => 'fasta');
$out2->write_seq($seq2);
$self->_query2_seq($seq2);
# Make sure you close things - this is what creates
# Out of filehandle errors
close($tfh2);
undef $tfh2;
}
return ($outfile1,$outfile2);
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
=cut
sub _setparams {
my ($self) = @_;
my $param_string;
foreach my $attr(@PROMOTERWISE_PARAMS){
my $value = $self->$attr();
next unless (defined $value);
my $attr_key = ' -'.(lc $attr);
$param_string .= $attr_key.' '.$value;
}
foreach my $attr(@PROMOTERWISE_SWITCHES){
my $value = $self->$attr();
next unless (defined $value);
my $attr_key = ' -'.(lc $attr);
$param_string .=$attr_key;
}
$param_string = $param_string." -hitoutput tab"; #specify the output option
return $param_string;
}
=head2 _query_pep_seq
Title : _query_pep_seq
Usage : Internal function, not to be called directly
Function: get/set for the query sequence
Example :
Returns :
Args :
=cut
sub _query1_seq {
my ($self,$seq) = @_;
if(defined $seq){
$self->{'_query1_seq'} = $seq;
}
return $self->{'_query1_seq'};
}
=head2 _subject_dna_seq
Title : _subject_dna_seq
Usage : Internal function, not to be called directly
Function: get/set for the subject sequence
Example :
Returns :
Args :
=cut
sub _query2_seq{
my ($self,$seq) = @_;
if(defined $seq){
$self->{'_query2_seq'} = $seq;
}
return $self->{'_query2_seq'};
}
1;
Jump to Line
Something went wrong with that request. Please try again.