Ace::Sequence::FeatureList - Lightweight Access to Features
# 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');
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.
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.
There are only two methods in Ace::Sequence::FeatureList.
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"; }
print $list->asString;
This dumps the list out in tab-delimited format. The order of columns is type, subtype, count.
Ace, Ace::Object, Ace::Sequence, Ace::Sequence::Feature, GFF
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.
To install Ace, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Ace
CPAN shell
perl -MCPAN -e shell install Ace
For more information on module installation, please visit the detailed CPAN module installation guide.