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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "LICENSE" .IX Header "LICENSE" Copyright [2015\-2018] EMBL-European Bioinformatics Institute .PP Licensed under the Apache License, Version 2.0 (the \*(L"License\*(R"); 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 \*(L"\s-1AS IS\*(R" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,\s0 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