Bio::Tools FootPrinter
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Summary
Bio::Tools::FootPrinter - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Bio::Root::IO
Bio::Root::Root
Bio::SeqFeature::Generic
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
_add_featureDescriptionCode
_parseDescriptionCode
_parse_predictionsDescriptionCode
_predictions_parsedDescriptionCode
newDescriptionCode
next_featureDescriptionCode
Methods description
_add_featurecode    nextTop
 Title   : _add_feature
Usage : $footprint->_add_feature($feat)
Function: Add feature to array
Returns : none
Args : none
_parsecodeprevnextTop
 Title   : _parse
Usage : $footprint->_parse($name,$seq,$pattern)
Function: do the actual parsing
Returns : Bio::SeqFeature::Generic
Args : none
_parse_predictionscodeprevnextTop
 Title   : _parse_predictions
Usage : my $r = $footprint->_parse_predictions
Function: do the parsing
Returns : none
Args : none
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
Usage : $footprint->_predictions_parsed(1)
Function: Get/Set for whether predictions parsed
Returns : 1/0
Args : none
newcodeprevnextTop
 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
next_featurecodeprevnextTop
 Title   : next_feature
Usage : my $r = $footprint->next_feature
Function: Get the next feature from parser data
Returns : Bio::SeqFeature::Generic
Args : none
Methods code
_add_featuredescriptionprevnextTop
sub _add_feature {
    my ($self,$feat) = @_;
    if($feat){
        push @{$self->{'_feature'}},$feat;
    }
}
_parsedescriptionprevnextTop
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 $feat; } 1;
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
  my ($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); $self->_predictions_parsed(1);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self,$val) = @_;
    if($val){
        $self->{'_predictions_parsed'} = $val;
    }
    return $self->{'_predictions_parsed'};
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

  return $self;
}
next_featuredescriptionprevnextTop
sub next_feature {
   my ($self) = @_;
   $self->_parse_predictions() unless $self->_predictions_parsed();
   return shift @{$self->{'_feature'}};
}
General documentation
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
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/
AUTHOR - Shawn Hoon Top
Email shawnh@fugu-sg.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _