Bio::Tools FootPrinter
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Summary
Bio::Tools::FootPrinter - write sequence features in FootPrinter format
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
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
This module writes sequence features in FootPrinter format.
See http://bio.cs.washington.edu/software.html for more details.
Methods
newDescriptionCode
next_featureDescriptionCode
_add_featureDescriptionCode
_parse_predictionsDescriptionCode
_predictions_parsedDescriptionCode
_parseDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::FootPrinter->new();
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
_add_featurecodeprevnextTop
 Title   : _add_feature
Usage : $footprint->_add_feature($feat)
Function: Add feature to array
Returns : none
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
_parsecodeprevnextTop
 Title   : _parse
Usage : $footprint->_parse($name,$seq,$pattern)
Function: do the actual parsing
Returns : Bio::SeqFeature::Generic
Args : none
Methods code
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'}};
}
_add_featuredescriptionprevnextTop
sub _add_feature {
    my ($self,$feat) = @_;
    if($feat){
        push @{$self->{'_feature'}},$feat;
    }
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
  my ($self) = @_;
  $/="";
  my ($seq,$second,$third,$name);
  while ($_ = $self->_readline) {
    chomp;
    my @array = split("\n",$_);
    if ($#array == 5) {
      # get rid of header
shift(@array); shift(@array); } if($#array == 3){ if($name){ $name=~s/>//;
my $feat = $self->_parse($name,$seq,$second,$third); $self->_add_feature($feat); } $name = shift @array; $seq = $array[0]; $second = $array[1]; $third = $array[2]; next; } $seq .= $array[0]; $third .= $array[2]; } $seq || return; $name=~s/>//;
my $feat = $self->_parse($name,$seq,$second,$third); $self->_add_feature($feat); $self->_predictions_parsed(1);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self,$val) = @_;
    if($val){
        $self->{'_predictions_parsed'} = $val;
    }
    return $self->{'_predictions_parsed'};
}
_parsedescriptionprevnextTop
sub _parse {
    my ($self,$name,$seq,$score,$pattern) = @_;
    my @char  = split('',$pattern);
    my @score = split('',$score);

    my ($prev,$word,@words,@word_scores,$word_score);

    my $i = 0;
    for my $c ( @char ) {
        if( ! $word) {
            $word .= $c;
            $prev = $c;
	    defined $score[$i] && 
		($score[$i] =~ /\d/) && ($word_score += $score[$i]);
        } elsif ($c eq $prev){
	    $word .=$c;
	    $prev  = $c;
	    defined $score[$i] && 
		($score[$i] =~ /\d/) && ($word_score += $score[$i]);
        } else {
            # remove words with only \s
$word=~s/\s+//g;
if ($word ne ''){ push @words, $word; push @word_scores, ($word_score/length($word));
} $word =$c; $prev = $c; $word_score = 0; defined $score[$i] && ($score[$i] =~ /\d/) && ($word_score += $score[$i]); } $i++; } $word =~s/\s+//g;
if( length($word) ){ push @words, $word; } my $last; my $feat = Bio::SeqFeature::Generic->new(-seq_id=>$name); my $offset = $i = 0; my $count = 1; for my $w (@words){ if(length($w) ) { my $index = index($pattern,$w,$offset); $offset = $index + length($w); my $subfeat = Bio::SeqFeature::Generic->new ( -seq_id =>"$name-motif".$count++, -start => $index+1, -end => $index+length($w), -source =>"FootPrinter", -score => $word_scores[$i] ); # ugh - not sure the sub_SeqFeature situation will
# be around forever- things should probably be
# grouped by a 'group' tag instead ala GFF3
# perhaps when Lincoln's API changes are
# made to SeqFeatures this will get changed
$feat->add_sub_SeqFeature($subfeat,'EXPAND'); } $i++; } my $priseq = Bio::PrimarySeq->new(-id=>$name,-seq=>$seq); $feat->attach_seq($priseq); return $feat; } 1;
}
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/wiki/Mailing_lists - About the mailing lists
Support Top
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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon Top
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _