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Ace/Sequence/Feature.pm  view on Meta::CPAN

  }

  # for efficiency/performance, we don't use superclass new() method, but modify directly
  # handling coordinates.  See SCRAPS below for what should be in here
  $strand = '+1' if $strand < 0 && $r_strand < 0;  # two wrongs do make a right
  ($start,$end) = ($end,$start) if $strand < 0;
  my $offset = $start - 1;
  my $length = ($end > $start) ? $end - $offset : $end - $offset - 2;

  # handle negative strands
  $offset ||= 0;
  $offset *= -1 if $r_strand < 0 && $strand != $r_strand;

  my $self= bless {
		   obj      => $ref,
		   offset   => $offset,
		   length   => $length,
		   parent   => $parent,
		   p_offset => $r_offset,
		   refseq   => [$ref,$r_offset,$r_strand],
		   strand   => $r_strand,
		   fstrand  => $strand,
		   absolute => $abs,
		   info     => {
				seqname=> $sourceseq,
				method => $method,
				type   => $type,
				score  => $score,
				frame  => $frame,
				group  => $group,
				db     => $db,
			       }
		  },$pack;
  return $self;
}

sub smapped { 1; }

# $_[0] is field name, $_[1] is self, $_[2] is optional replacement value
sub _field {
  my $self = shift;
  my $field = shift;
  my $v = $self->{info}{$field};
  $self->{info}{$field} = shift if @_;
  return if defined $v && $v eq '.';
  return $v;
}

sub strand { return $_[0]->{fstrand} }

sub seqname   { 
  my $self = shift;
  my $seq = $self->_field('seqname');
  $self->db->fetch(Sequence=>$seq); 
}

sub method    { shift->_field('method',@_) }  # ... I prefer "method"
sub subtype   { shift->_field('method',@_) }  # ... or even "subtype"
sub type      { shift->_field('type',@_)   }  # ... I prefer "type"
sub score     { shift->_field('score',@_)  }  # float indicating some sort of score
sub frame     { shift->_field('frame',@_)  }  # one of 1, 2, 3 or undef
sub info      {                  # returns Ace::Object(s) with info about the feature
  my $self = shift;
  unless ($self->{group}) {
    my $info = $self->{info}{group} || 'Method "'.$self->method.'"';
    $info =~ s/(\"[^\"]*);([^\"]*\")/$1$;$2/g;
    my @data = split(/\s*;\s*/,$info);
    foreach (@data) { s/$;/;/g }
    $self->{group} = [map {$self->toAce($_)} @data];
  }
  return wantarray ? @{$self->{group}} : $self->{group}->[0];
}

# bioperl compatibility
sub primary_tag { shift->type(@_)    }
sub source_tag  { shift->subtype(@_) }

sub db { # database identifier (from Ace::Sequence::Multi)
  my $self = shift;
  my $db = $self->_field('db',@_);
  return $db || $self->SUPER::db;
}

sub group  { $_[0]->info; }
sub target { $_[0]->info; }

sub asString {
  my $self = shift;
  my $name = $self->SUPER::asString;
  my $type = $self->type;
  return "$type:$name";
}

# unique ID
sub id {
  my $self = shift;
  my $source = $self->source->name;
  my $start = $self->start;
  my $end = $self->end;
  return "$source/$start,$end";
}

# map info into a reasonable set of ace objects
sub toAce {
    my $self = shift;
    my $thing = shift;
    my ($tag,@values) = $thing=~/(\"[^\"]+?\"|\S+)/g;
    foreach (@values) { # strip the damn quotes
      s/^\"(.*)\"$/$1/;  # get rid of leading and trailing quotes
    }
    return $self->tag2ace($tag,@values);
}

# synthesize an artificial Ace object based on the tag
sub tag2ace {
    my $self = shift;
    my ($tag,@data) = @_;

    # Special cases, hardcoded in Ace GFF code...
    my $db = $self->db;;
    my $class = $db->class;

Ace/Sequence/Feature.pm  view on Meta::CPAN

=item method()

=item subtype()

  $source = $feature->source;

These three methods are all synonyms for the same thing.  They return
the second field of the GFF format, called "source" in the
documentation.  This is usually the method or algorithm used to
predict the feature, such as "GeneFinder" or "tRNA" scan.  To avoid
ambiguity and enhance readability, the method() and subtype() synonyms
are also recognized.

=item feature()

=item type()

  $type = $feature->type;

These two methods are also synonyms.  They return the type of the
feature, such as "exon", "similarity" or "Predicted_gene".  In the GFF
documentation this is called the "feature" field.  For readability,
you can also use type() to fetch the field.

=item abs_start()

  $start = $feature->abs_start;

This method returns the absolute start of the feature within the
sequence segment indicated by seqname().  As in the I<Ace::Sequence>
method, use start() to obtain the start of the feature relative to its
source.

=item abs_start()

  $start = $feature->abs_start;

This method returns the start of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited start() method to obtain the
start of the feature relative to its source sequence (the
I<Ace::Sequence> from which it was originally derived).

=item abs_end()

  $start = $feature->abs_end;

This method returns the end of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited end() method to obtain the end
of the feature relative to the I<Ace::Sequence> from which it was
derived.

=item score()

  $score = $feature->score;

For features that are associated with a numeric score, such as
similarities, this returns that value.  For other features, this
method returns undef.

=item strand()

  $strand = $feature->strand;

Returns the strandedness of this feature, either "+1" or "-1".  For
features that are not stranded, returns 0.

=item reversed()

  $reversed = $feature->reversed;

Returns true if the feature is reversed relative to its source
sequence.

=item frame()

  $frame = $feature->frame;

For features that have a frame, such as a predicted coding sequence,
returns the frame, either 0, 1 or 2.  For other features, returns undef.

=item group()

=item info()

=item target()

  $info = $feature->info;

These methods (synonyms for one another) return an Ace::Object
containing other information about the feature derived from the 8th
field of the GFF format, the so-called "group" field.  The type of the
Ace::Object is dependent on the nature of the feature.  The
possibilities are shown in the table below:

  Feature Type           Value of Group Field
  ------------            --------------------
  
  note                   A Text object containing the note.
  
  similarity             An Ace::Sequence::Homology object containing
                         the target and its start/stop positions.

  intron                 An Ace::Object containing the gene from 
  exon                   which the feature is derived.
  misc_feature

  other                  A Text object containing the group data.

=item asString()

  $label = $feature->asString;

Returns a human-readable identifier describing the nature of the
feature.  The format is:

 $type:$name/$start-$end

for example:

 exon:ZK154.3/1-67

This method is also called automatically when the object is treated in
a string context.

=back

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,L<Ace::Sequence::Homol>,
L<Ace::Sequence::FeatureList>, L<GFF>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify