Ace::Sequence::FeatureList.3pm

Langue: en

Version: 2000-06-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

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 <lstein@w3.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 it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.