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ACE::SEQUENCE::FEATURELIST(3PM) - Linux man page online | Library functions

Lightweight Access to Features.

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2017-11-24
Ace::Sequence::FeatureList(3pm)User Contributed Perl DocumentationAce::Sequence::FeatureList(3pm)

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 <@w3.org> with extensive help from Jean Thierry-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.
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