package Ace::Sequence::FeatureList;
use overload '""' => 'asString';
sub new {
local $^W = 0; # to prevent untrackable uninitialized variable warning
my $package =shift;
my @lines = split("\n",$_[0]);
my (%parsed);
foreach (@lines) {
next if m!^//!;
my ($minor,$major,$count) = split "\t";
next unless $count > 0;
$parsed{$major}{$minor} += $count;
$parsed{_TOTAL} += $count;
}
return bless \%parsed,$package;
}
# no arguments, scalar context -- count all features
# no arguments, array context -- list of major types
# 1 argument, scalar context -- count of major type
# 1 argument, array context -- list of minor types
# 2 arguments -- count of subtype
sub types {
my $self = shift;
my ($type,$subtype) = @_;
my $count = 0;
unless ($type) {
return wantarray ? grep !/^_/,keys %$self : $self->{_TOTAL};
}
unless ($subtype) {
return keys %{$self->{$type}} if wantarray;
foreach (keys %{$self->{$type}}) {
$count += $self->{$type}{$_};
}
return $count;
}
return $self->{$type}{$subtype};
}
# human-readable summary table
sub asString {
my $self = shift;
my ($type,$subtype);
for my $type ( sort $self->types() ) {
for my $subtype (sort $self->types($type) ) {
print join("\t",$type,$subtype,$self->{$type}{$subtype}),"\n";
}
}
}
1;
=head1 NAME
Ace::Sequence::FeatureList - Lightweight Access to Features
=head1 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');
=head1 DESCRIPTION
I<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.
=head1 OBJECT CREATION
You will not ordinarily create an I<Ace::Sequence::FeatureList> object
directly. Instead, objects will be created by calling a
I<Ace::Sequence> object's feature_list() method. If you wish to
create an I<Ace::Sequence::FeatureList> object directly, please consult
the source code for the I<new()> method.
=head1 OBJECT METHODS
There are only two methods in I<Ace::Sequence::FeatureList>.
=over 4
=item 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";
}
=item asString()
print $list->asString;
This dumps the list out in tab-delimited format. The order of columns
is type, subtype, count.
=back
=head1 SEE ALSO
L<Ace>, L<Ace::Object>, L<Ace::Sequence>,
L<Ace::Sequence::Feature>, L<GFF>
=head1 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.
=cut