bio-tabix

Ruby binding for the tabix file indexing routines within the samtools package samtools.sourceforge.net/

Tabix provides utilities for indexing and subsequently querying regions of interest from large tab delimited files.

Files are indexed on three columns: [group, pos1, pos2] and must be position sorted

This gem was modeled on the bio-samtools gem: github.com/helios/bioruby-samtools

Installation

gem install bio-tabix

Usage

Compress your file

The following command will run the bgzip utility. You must supply input and output filenames. If you don't compress your data first, it will be compressed when the file is opened appending '.bgzf' to the filename.

Bio::Tabix::TFile.compress(in_file,compressed_file)

Index the file

Build an index by supplying the required columns. If you don't create an index the open method will use the default options. The opts parameter takes a hash of index build options

  • :s => sequence/group column [1]

  • :b => beginning range column [2]

  • :e => ending range column. Can equal :b [3]

  • :meta_char => comment character [#]

  • :line_skip => number of initial lines to ignore [0]

tabix_file = Bio::Tabix::TFile.build_index(compressed_file, {:s => group_col, :b => pos1_col, :e => pos2_col})

Open your file

Create a new TFile instance and open it.

tabix_file = Bio::Tabix::TFile.open(compressed_file)

Create a proc or lambda

This will be called with the value of each fileline

my_func = lambda do |line|
 # convert text to array and print column index 3
 puts line.split("\t")[3]
end

Process a region

Choose a group and range for your function and process it

tabix_file.process_region('g2', 4, 10, my_func)

Example

File

g1	1	3	a1	b1
g1	2	3	a2	b2
g1	3	4	a3	b3
...
g2	1	2	A1	B1
g2	2	4	A2	B2
g2	3	5	A3	B3
g2	4	6	A4	B4
...

Output

A2
A3
A4

Dependencies:

Contributing to bio-tabix

  • Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.

  • Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.

  • Fork the project.

  • Start a feature/bugfix branch.

  • Commit and push until you are happy with your contribution.

  • Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Copyright

Copyright © 2012 Nicholas A Thrower. See LICENSE.txt for further details.