Ace::Sequence::FeatureList

NAME

Ace::Sequence::FeatureList - Lightweight Access to Features

SYNOPSIS

    # get a megabase from the middle of chromosome I
    $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                              -db     => $db,
                              -offset => 3_000_000,
                              -length => 1_000_000);
    # find out what's there
    $list = $seq->feature_list;
    # Scalar context: count all the features
    $feature_count = $list->types;
    # Array context: list all the feature types
    @feature_types = $list->types;
    # Scalar context, 1 argument.  Count this type
    $gene_cnt = $list->types('Predicted_gene');
    print "There are $gene_cnt genes here.\n";
    # Array context, 1 argument.  Get list of subtypes
    @subtypes = $list->types('Predicted_gene');
    # Two arguments. Count type & subtype
    $genefinder_cnt = $list->types('Predicted_gene','genefinder');

DESCRIPTION

Ace::Sequence::FeatureList is a small class that provides statistical information about sequence features. From it you can obtain summary counts of the features and their types within a selected region.

OBJECT CREATION

You will not ordinarily create an Ace::Sequence::FeatureList object directly. Instead, objects will be created by calling a Ace::Sequence object's feature_list() method. If you wish to create an Ace::Sequence::FeatureList object directly, please consult the source code for the new() method.

OBJECT METHODS

There are only two methods in Ace::Sequence::FeatureList.

type()

This method has five distinct behaviors, depending on its context and the number of parameters. Usage should be intuitive

 Context       Arguments       Behavior
 -------       ---------       --------
 scalar         -none-         total count of features in list
 array          -none-         list feature types (e.g. "exon")
 scalar          type          count features of this type
 array           type          list subtypes of this type
 -any-       type,subtype      count features of this type & subtype
    

For example, this code fragment will count the number of exons present on the list:

  $exon_count = $list->type('exon');
    

This code fragment will count the number of exons found by "genefinder":

  $predicted_exon_count = $list->type('exon','genefinder');
    

This code fragment will print out all subtypes of "exon" and their counts:

  for my $subtype ($list->type('exon')) {
      print $subtype,"\t",$list->type('exon',$subtype),"\n";
  }
    

asString()

  print $list->asString;
    

This dumps the list out in tab-delimited format. The order of columns is type, subtype, count.

SEE ALSO

Ace, Ace::Object, Ace::Sequence, Ace::Sequence::Feature, GFF

AUTHOR

Lincoln Stein <[email protected]> with extensive help from Jean Thierry-Mieg <[email protected]> Copyright (c) 1999, Lincoln D. Stein This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.