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

 Title   : _parse
 Usage   : $footprint->_parse($name,$seq,$pattern)
 Function: do the actual parsing
 Returns : Bio::SeqFeature::Generic
 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   : 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

Methods code

sub _add_feature {

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

}

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;
    
}

1;

}

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 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'}};

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  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 _