Bio::Tools::Run::Alignment Exonerate
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Summary
Bio::Tools::Run::Alignment::Exonerate
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::SearchIO
Bio::Tools::Run::WrapperBase
Inherit
Bio::Factory::ApplicationFactoryI Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Alignment::Exonerate;
use Bio::SeqIO;
my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta'); my $query = $qio->next_seq(); my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta'); my $target = $sio->next_seq(); #exonerate parameters can all be passed via arguments parameter. #parameters passed are not checked for validity my $run = Bio::Tools::Run::Alignment::Exonerate-> new(arguments=>'--model est2genome --bestn 10'); my $searchio_obj = $run->run($query,$target); while(my $result = $searchio->next_result){ while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { print $hsp->start."\t".$hsp->end."\n"; } } }
Description
Wrapper for Exonerate alignment program. You can get exonerate at
http://www.ebi.ac.uk/~guy/exonerate/. This wrapper is written without
parameter checking. All parameters are passed via the arugment
parameter that is passed in the constructor. See SYNOPSIS. For
exonerate parameters, run exonerate --help for more details.
Methods
program_nameDescriptionCode
program_dirDescriptionCode
AUTOLOAD
No description
Code
newDescriptionCode
versionDescriptionCode
runDescriptionCode
_input()
No description
Code
_runDescriptionCode
_writeInputDescriptionCode
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
newcodeprevnextTop
 Title   : new
Usage : my $factory= Bio::Tools::Run::Phrap->new();
Function: creates a new Phrap factory
Returns: Bio::Tools::Run::Phrap
Args :
versioncodeprevnextTop
 Title   : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
runcodeprevnextTop
 Title   :   run()
Usage : my $feats = $factory->run($seq)
Function: Runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
_runcodeprevnextTop
 Title   :   _run
Usage : $factory->_run()
Function: Makes a system call and runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeInputcodeprevnextTop
 Title   :   _writeInput
Usage : $factory->_writeInput($query,$target)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI
_setparamscodeprevnextTop
 Title   :  _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
Methods code
program_namedescriptionprevnextTop
sub program_name {
    return 'exonerate';
}
program_dirdescriptionprevnextTop
sub program_dir {
    return Bio::Root::IO->catfile($ENV{EXONERATEDIR}) if $ENV{EXONERATEDIR};
}
AUTOLOADdescriptionprevnextTop
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};
}
newdescriptionprevnextTop
sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
 
       my ($attr, $value);
       while (@args)  {
           $attr =   shift @args;
           $value =  shift @args;
           next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) { $self->executable($value); next; } $self->$attr($value); } return $self;
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    my $exe;
    return undef unless $exe = $self->executable;
    my $string = `$exe -v` ;
    #exonerate from exonerate version 2.0.0\n...
my ($version) = $string =~ /exonerate version ([\d+\.]+)/m; $version =~ s/\.(\d+)$/$1/; return $version || undef;
}
rundescriptionprevnextTop
sub run {
    my ($self,$query,$target) = @_;
    my @feats;
    my ($file1) = $self->_writeInput($query);
    my ($file2) = $self->_writeInput($target);
    my $assembly = $self->_run($file1,$file2);
    return $assembly;
}
_input()descriptionprevnextTop
sub _input() {
     my ($self,$infile1) = @_;
     $self->{'input'} = $infile1 if(defined $infile1);
     return $self->{'input'};
}
_rundescriptionprevnextTop
sub _run {
     my ($self,$query,$target)= @_;

     my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
     my $param_str = $self->_setparams." ".$self->arguments;
     my $str = $self->executable." $param_str $query $target "." > $outfile";
     $self->debug( "$str\n");
     my $status = system($str);
     $self->throw( "Exonerate call ($str) crashed: $?\n ") unless $status==0;
     my $filehandle;
     my $exonerate_obj = Bio::SearchIO->new(-file=>"$outfile",-format=>'exonerate');

     close($tfh);
     undef $tfh;
     unlink $outfile;

     return $exonerate_obj;
}
_writeInputdescriptionprevnextTop
sub _writeInput {
    my ($self,$query) = @_;
    my ($fh,$infile1);
    if (ref($query) =~ /ARRAY/i) {
      my @infilearr;
      ($fh, $infile1) = $self->io->tempfile();
      my $temp = Bio::SeqIO->new( -file => ">$infile1",
                                  -format => 'Fasta' );
      foreach my $seq1 (@$query) {
        unless ($seq1->isa("Bio::PrimarySeqI")) {
          return 0;
        }
        $temp->write_seq($seq1);
        push @infilearr, $infile1;
      }
    }
    elsif($query->isa("Bio::PrimarySeqI")) {
      ($fh, $infile1) = $self->io->tempfile();
      my $temp = Bio::SeqIO->new( -file => ">$infile1",
                                  -format => 'Fasta' );
      $temp->write_seq($query);
    }
    else {
      $infile1 = $query;
    }
    return $infile1;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self) = @_;
    my $param_string = '';
    foreach my $attr(@EXONERATE_PARAMS){
        next if($attr=~/PROGRAM/);
        my $value = $self->$attr();
        next unless (defined $value);
        my $attr_key = ' -'.(lc $attr);
        $param_string .= $attr_key.' '.$value;
    }
    return $param_string;
}

1;
}
General documentation
PROGRAM VERSIONSTop
The tests have been shown to pass with exonorate versions 2.0 - 2.2.
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 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
SupportTop
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:
  http://bugzilla.open-bio.org/
AUTHOR - Shawn HoonTop
  Email shawnh-at-stanford.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
_inputTop
 Title   :   _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :