LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

NAME

Bio::DB::HTS::Tabix - Object oriented access to the underlying tbx C methods

SYNOPSIS

use feature qw( say );
use Bio::DB::HTS::Tabix;

my $tabix = Bio::DB::HTS::Tabix->new( filename => "gerp_plus_plus_31July2014.gz" );

say $tabix->header;
my $iter = $tabix->query("1:4000005-4000009");

while ( my $n = $iter->next ) {
    say $n;
}
$tabix->close;

DESCRIPTION

A high level object oriented interface to the htslib tabix (tbx.h) api. Currently it only supports retrieving regions from a tabixed file, because that's all I needed it for.

Attributes

filename

The gzipped file you want to query. Must have a filename.tbi (the index is not created automatically)

Methods

header

Returns all the header lines as a single scalar from the tabixed file

query

Takes a single region like: '1:4000005-4000009' or '12:5000000'. The coordinate format is 0 or 1-based for start and stop positions depending on how the Tabix index file was created - by default this is 1.

The index for remote files will be downloaded to the system temporary directory by default. Set use_tmp_dir to 0 to download to the current working directory instead.

Here are some examples showing Tabix.

use Bio::DB::HTS::Tabix;

my $tabix = Bio::DB::HTS::Tabix->new(filename => $file, use_tmp_dir => 1);

# Calling region 1

$iter = $tabix->query("1");
printf("Calling region 1\n" );
while(my $l = $iter->next) {
  print $l, "\n";
}
Gives:
1       4000000 4000000 -0.972
1       4000001 4000001 -0.153
1       4000002 4000002 -2.15
1       4000003 4000003 -1.17
1       4000003 4000006 -3.6
1       4000006 4000007 -6.7
1       4000007 4000009 -7.9


#Calling a range
$iter = $tabix->query("1:4000003-4000006");
gives
1       4000003 4000003 -1.17
1       4000003 4000006 -3.6
1       4000006 4000007 -6.7

#Calling region 1:4000003 to end of region 1
$iter = $tabix->query("1:4000003");
gives
1       4000003 4000003 -1.17
1       4000003 4000006 -3.6
1       4000006 4000007 -6.7
1       4000007 4000009 -7.9

#Calling single location 1:4000002
$iter = $tabix->query("1:4000002-4000002");
gives
1       4000002 4000002 -2.15

Returns a Bio::DB::HTS::Tabix::Iterator for the specified region

seqnames

Returns an array ref of chromosomes that are in the indexed file

AUTHOR

Alex Hodgkins Rishi Nag <rishi@ebi.ac.uk>