Summary

Bio::Tools::FootPrinter - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

    use Bio::Tools::FootPrinter;

    my $tool = Bio::Tools::FootPrinter->new(-file=>"footprinter.out");

    while (my $result = $tool->next_feature){
      foreach my $feat($result->sub_SeqFeature){
        print $result->seq_id."\t".$feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
      }
    }

Description

A parser for FootPrinter output

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::FootPrinter();
 Function: Builds a new Bio::Tools::FootPrinter object 
 Returns : Bio::Tools::FootPrinter
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

 Title   : next_feature
 Usage   : my $r = $footprint->next_feature
 Function: Get the next feature from parser data
 Returns : Bio::SeqFeature::Generic 
 Args    : none

 Title   : _add_feature
 Usage   : $footprint->_add_feature($feat)
 Function: Add feature to array
 Returns : none
 Args    : none

 Title   : _parse_predictions
 Usage   : my $r = $footprint->_parse_predictions
 Function: do the parsing 
 Returns : none 
 Args    : none

 Title   : _predictions_parsed
 Usage   : $footprint->_predictions_parsed(1)
 Function: Get/Set for whether predictions parsed
 Returns : 1/0
 Args    : none

 Title   : _parse
 Usage   : $footprint->_parse($name,$seq,$pattern)
 Function: do the actual parsing
 Returns : Bio::SeqFeature::Generic
 Args    : none

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);

  return $self;

}

sub next_feature {

   my ($self) = @_;
   $self->_parse_predictions() unless $self->_predictions_parsed();
   return shift @{$self->{'_feature'}};

}

sub _add_feature {

    my ($self,$feat) = @_;
    if($feat){
        push @{$self->{'_feature'}},$feat;
    }

}

sub _parse_predictions {

  my ($self) = @_;
  $/="";
  my ($seq,$third,$name);
  while ($_ = $self->_readline) {
    chomp;
    my @array = split("\n",$_);
    if($#array == 3){
        if($name){
            $name=~s/>//;
            my $feat = $self->_parse($name,$seq,$third);
            $self->_add_feature($feat);
        }
        $name = shift @array;
        $seq=$array[0];
        $third=$array[2];
        next;
    }
    $seq.=$array[0];
    $third.=$array[2];
  }
  $name=~s/>//;
  my $feat = $self->_parse($name,$seq,$third);
  $self->_add_feature($feat);

  $self->_predictions_parsed(1);

}

sub _predictions_parsed {

    my ($self,$val) = @_;
    if($val){
        $self->{'_predictions_parsed'} = $val;
    }
    return $self->{'_predictions_parsed'};

}

sub _parse {

  my ($self,$name,$seq,$pattern) = @_;
    my @char = split('',$pattern);
    my $prev;
   my $word;
    my @words;
    foreach my $c(@char){
        if(!$word){
            $word .= $c;
            $prev = $c;
            next;
        }
        if ($c eq $prev){
          $word.=$c;
          $prev = $c;
        }
        else {
            #remove words with only \s
            $word=~s/\s+//g;
            if ($word ne ''){
              push @words, $word;
            }
            $word=$c;
           $prev = $c;
           
        }
    }
    $word=~s/\s+//g;
    if($word ne ''){
      push @words, $word;
    }
    my $last;
    my $feat = new Bio::SeqFeature::Generic(-seq_id=>$name);
    my $offset=0;
    foreach my $w(@words){
        if($w !~ /^$/){
          my $index = index($pattern,$w,$offset);
          $offset = $index + length($w);
          my $subfeat = new Bio::SeqFeature::Generic ( -seq_id=>$name,
                                                    -start => $index+1, 
                                                    -end =>$index+length($w),
                                                    -source=>"FootPrinter");
          $feat->add_sub_SeqFeature($subfeat,'EXPAND');
        }
    }
    my $priseq = Bio::PrimarySeq->new(-id=>$name,-seq=>$seq);
    $feat->attach_seq($priseq);
    return $feat;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
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of the bugs and their resolution. Bug reports can be submitted via
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  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email shawnh@fugu-sg.org
Describe contact details here

Additional contributors names and emails here

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