Toolbar

Summary

Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows
for alignment of cdna to genomic sequences

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

  use Bio::Tools::Run::Alignment::Sim4;

  my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>"mouse_cdna.fa",genomic_seq=>"mouse_genomic.fa");
  my $sim4 = Bio::Tools::Run::Alignment::Sim4->new(@params);

  my @exon_sets = $sim4->align;

  foreach my $set(@exon_sets){
    foreach my $exon($set->sub_SeqFeature){
        print $exon->start."\t".$exon->end."\t".$exon->strand."\n";
        print "\tMatched ".$exon->est_hit->seq_id."\t".$exon->est_hit->start."\t".$exon->est_hit->end."\n";
    }
  }

  One can also provide a est database

 $sio = Bio::SeqIO->new(-file=>"est.fa",-format=>"fasta");
 @est_seq=();
 while(my $seq = $sio->next_seq){
         push @est_seq,$seq;
 }

 my @exon_sets = $factory->align(\@est_seq,$genomic);

Description

Sim4 program is developed by Florea et al. for aligning cdna/est
sequence to genomic sequences
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W.
A computer program for aligning a cDNA sequence with a genomic DNA sequence.
Genome Res 1998 Sep;8(9):967-74
The program is available for download here:
http://globin.cse.psu.edu/

Methods

Methods description

 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

 Title   : version
 Usage   : not supported 
 Function: Cannot determine from program 
 Example :
 Returns : float or undef
 Args    : none

 Title   : align
 Usage   :
            $cdna = 't/data/cdna.fa';
            $genomic = 't/data/cdna.fa';
            @exon_set = $factory->align($cdna,$genomic);
          or
            #@seq_array is array of Seq objs
            $cdna = \@seq_array; 
            @exon_set = $factory->align($cdna,$genomic);
          of
            @exon_set = $factory->align($cdna->[0],$genomic)

 Function: Perform a Sim4  alignment
 Returns : An array of Bio::SeqFeature::Generic objects which has
           exons as sub seqfeatures.
 Args    : Name of two files containing fasta sequences, 
           or 2 Bio::SeqI objects
           or a combination of both
           first is assumed to be cdna
           second is assumed to be genomic
           More than one cdna may be provided. If an object,
           assume that its an array ref.

 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:   makes actual system call to Sim4 program
 Example :
 Returns : nothing; Sim4  output is written to a temp file
 Args    : Name of a file containing a set of unaligned fasta sequences
           and hash of parameters to be passed to Sim4

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:   Create input file for Sim4 program
 Example :
 Returns : name of file containing Sim4 data input
 Args    : Seq or Align object reference or input file name

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:   Create parameter inputs for Sim4 program
 Example :
 Returns : parameter string to be passed to Sim4 
           during align or profile_align
 Args    : name of calling object

Methods code

BEGIN {

    @SIM4_PARAMS= qw(A W X K C R D H P N B); 
    @OTHER_PARAMS= qw(CDNA_SEQ GENOMIC_SEQ OUTFILE);
    @OTHER_SWITCHES = qw(SILENT QUIET VERBOSE); 

    # Authorize attribute fields
    foreach my $attr ( @SIM4_PARAMS, @OTHER_PARAMS,
                       @OTHER_SWITCHES) { $OK_FIELD{$attr}++;

}

sub program_name {

  return 'sim4';

}

sub program_dir {

  return Bio::Root::IO->catfile($ENV{SIM4DIR}) if $ENV{SIM4DIR};

}

sub new {

  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);
  # to facilitiate tempfile cleanup
  $self->io->_initialize_io();
  $self->A(0); # default
  my ($attr, $value);
  
  while (@args) {
    $attr =   shift @args;
    $value =  shift @args;
    if ($attr =~/est_first/i )  {      #NEW
       $self->{est_first} = $value;    #NEW
       next;                           #NEW
    }                                  #NEW
    next if( $attr =~ /^-/ ); # don't want named parameters
    if ($attr =~/'PROGRAM'/i )  {
      $self->executable($value);
      next;
    }
    $self->$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};

}

sub version {

    my ($self) = @_;
    return undef;

}

sub align {

    my ($self,$cdna,$genomic) = @_;

    $self->cdna_seq($cdna) if $cdna;
    $self->throw("Need to provide a cdna sequence") unless $self->cdna_seq;

    $self->genomic_seq($genomic) if $genomic;
    $self->throw("Need to provide a genomic sequence") unless $self->genomic_seq;
    
    my ($temp,$infile1, $infile2, $est_first,$seq);
    my ($attr, $value, $switch);

# Create input file pointer
    ($est_first,$infile1,$infile2)= $self->_setinput($self->cdna_seq,$self->genomic_seq);
    if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 sequences in align!");}

# Create parameter string to pass to Sim4 program
    my $param_string = $self->_setparams();

# run Sim4 
    my @exon_sets = $self->_run($est_first,$infile1,$infile2,$param_string);
    return @exon_sets;
}

#################################################
#internal methods

}

sub _run {

    my ($self,$estfirst,$infile1,$infile2,$param_string) = @_;
    my $instring;
    $self->debug( "Program ".$self->executable."\n");
    if(! $self->outfile){
        my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir);
	close($tfh);
	undef $tfh;
        $self->outfile($outfile);
    }
    my $outfile = $self->outfile(); 
    my $commandstring = $self->executable." $infile1 $infile2 $param_string > $outfile";
    if($self->quiet || $self->silent || ($self->verbose < 0)){
      $commandstring .= " 2>/dev/null";
    }
    $self->debug( "Sim4 command = $commandstring");
    my $status = system($commandstring);
    $self->throw( "Sim4 call ($commandstring) crashed: $?\n ") unless $status==0;

    #use Sim4 parser
    my $sim4_parser = Bio::Tools::Sim4::Results->new(-file=>$outfile,-estfirst=>$estfirst);
    my @out;
    while(my $exonset = $sim4_parser->next_exonset){
        push @out, $exonset;
    }
    return @out;

}

sub _setinput {

  my ($self, $cdna,$genomic) = @_;
  my ($infilename, $seq, $temp, $tfh1,$tfh2,$outfile1,$outfile2);
  #my $estfirst=1;
  my $estfirst= defined($self->{est_first}) ? $self->{_est_first} : 1;
  my ($cdna_file,$genomic_file);
  #a sequence obj
  if(ref($cdna)) {
      my @cdna = ref $cdna eq "ARRAY" ? @{$cdna} : ($cdna);
      ($tfh1,$cdna_file) = $self->io->tempfile(-dir=>$self->tempdir);
      my $seqio = Bio::SeqIO->new(-fh=>$tfh1,-format=>'fasta');
      foreach my $c (@cdna){
	  $seqio->write_seq($c);
      }
      close $tfh1;
      undef $tfh1;

      #if we have a est database, then input will  go second
      if($#cdna > 0){
	  $estfirst=0;
      }
  }
  else {
     my $sio = Bio::SeqIO->new(-file=>$cdna,-format=>"fasta");
     my $count = 0;
     while(my $seq = $sio->next_seq){
         $count++;
     }
     $estfirst = $count > 1 ? 0:1;
     $cdna_file = $cdna;
  }
  if( ref($genomic) ) {
      ($tfh1,$genomic_file) = $self->io->tempfile(-dir=>$self->tempdir);
      my $seqio = Bio::SeqIO->new(-fh=>$tfh1,-format=>'fasta');
      $seqio->write_seq($genomic);
      close $tfh1;
      undef $tfh1;
  }
  else {
      $genomic_file = $genomic;
  }
  return ($estfirst,$cdna_file,$genomic_file) if $estfirst;
  return ($estfirst,$genomic_file,$cdna_file);

}

sub _setparams {

    my ($attr, $value, $self);

    $self = shift;

    my $param_string = "";
    for  $attr ( @SIM4_PARAMS ) {
      $value = $self->$attr();
      next unless (defined $value);
      my $attr_key = uc $attr; #put params in format expected by Sim4 
      $attr_key = ' '.$attr_key;
      $param_string .= $attr_key.'='.$value;
    }

    return $param_string;
}

1; # Needed to keep compiler happy

}

General documentation

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

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.

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/

Email shawnh@fugu-sg.org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _