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.IX Title "Bio::DB::HTS::Tabix 3pm"
.TH Bio::DB::HTS::Tabix 3pm 2024-03-07 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH LICENSE
.IX Header "LICENSE"
Copyright [2015\-2018] EMBL-European Bioinformatics Institute
.PP
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
.PP
.Vb 1
\&     http://www.apache.org/licenses/LICENSE\-2.0
.Ve
.PP
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.
.SH NAME
Bio::DB::HTS::Tabix \- Object oriented access to the underlying tbx C methods
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\&    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;
.Ve
.SH DESCRIPTION
.IX Header "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.
.SS Attributes
.IX Subsection "Attributes"
.ie n .IP """filename""" 12
.el .IP \f(CWfilename\fR 12
.IX Item "filename"
The gzipped file you want to query. Must have a filename.tbi (the index is not created automatically)
.SS Methods
.IX Subsection "Methods"
.ie n .IP """header""" 12
.el .IP \f(CWheader\fR 12
.IX Item "header"
Returns all the header lines as a single scalar from the tabixed file
.ie n .IP """query""" 12
.el .IP \f(CWquery\fR 12
.IX Item "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.
.Sp
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.
.Sp
Here are some examples showing Tabix.
.Sp
.Vb 1
\&    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\en" );
\&    while(my $l = $iter\->next) {
\&      print $l, "\en";
\&    }
\&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
.Ve
.Sp
Returns a Bio::DB::HTS::Tabix::Iterator for the specified region
.ie n .IP """seqnames""" 12
.el .IP \f(CWseqnames\fR 12
.IX Item "seqnames"
Returns an array ref of chromosomes that are in the indexed file
.SH AUTHOR
.IX Header "AUTHOR"
Alex Hodgkins
Rishi Nag <rishi@ebi.ac.uk>