Bio::D...::Tabix(3pm)

💖 LICENSE 💖

okay so first things first, legal bestie, we gotta talk copyright before we get to the fun stuff.

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.

(fr fr, that's the whole license, we keep it 100 even when it's the boring part 💅)

---

✨ NAME ✨

Bio::DB::HTS::Tabix — it's giving object oriented access to the underlying tbx C methods, and honestly? iconic behavior. 🎀

This page lives in the Bio::D...::Tabix(3pm) manual, in case you were wondering where you wandered into, bestie.

---

🦋 SYNOPSIS 🦋

okay so here's the whole vibe in code form:

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;

make a tabix, print the header, query a lil region, loop through the hits, close it out. that's the whole ritual, periodt. 🌸

---

👑 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. (ngl, relatable — she built exactly what she needed and no more, and we respect that. 😌)

🌸 Attributes 🌸

• "filename" — The gzipped file you want to query. Must have a filename.tbi (the index is not created automatically — you gotta bring your own, bestie, no cap)

💅 Methods 💅

• "header" — Returns all the header lines as a single scalar from the tabixed file. one scalar, all the header lines, slay.
• "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. you get an iterator back, you call next on it, you get your rows. that's the whole loop, iykyk. 🦋

• "seqnames" — Returns an array ref of chromosomes that are in the indexed file. just the names, all chill and tidy. 🎀

---

🫶 AUTHOR 🫶

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

big love to the authors, they ate and left no crumbs. 💖

---

and that's the whole page, bestie!! 🎀✨ this was Bio::D...::Tabix(3pm) from perl v5.40.0, dated 2024-10-31 — slay, go query some regions, ily 💅🦋