https://github.com/arq5x/grabix

a wee tool for random access into BGZF files.
https://github.com/arq5x/grabix

Last synced: 3 months ago
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a wee tool for random access into BGZF files.

• Host: GitHub
• URL: https://github.com/arq5x/grabix
• Owner: arq5x
• License: mit
• Created: 2012-05-22T13:53:22.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2018-05-10T17:41:12.000Z (over 6 years ago)
• Last Synced: 2024-10-14T15:14:36.165Z (3 months ago)
• Language: C
• Size: 642 KB
• Stars: 84
• Watchers: 5
• Forks: 12
• Open Issues: 17
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• Awesome-Bioinformatics - grabix - A wee tool for random access into BGZF files. (Data Processing / Command Line Utilities)

README

        
grabix - a wee tool for random access into BGZF files.

======================================================

``grabix`` leverages the fantastic BGZF library in ``samtools`` to provide random access into

text files that have been compressed with ``bgzip``.  ``grabix`` creates it's own index (.gbi)

of the bgzipped file.  Once indexed, one can extract arbitrary lines from the file with the ``grab`` command.  Or choose random lines with the, well, ``random`` command.

There's a ton of room for improvement, but I needed something quickly in support of a side project.

Here's a brief example using the ``simrep.chr1.bed`` file provided in the repository.

	# 1. compress the file with bgzip

	bgzip simrep.chr1.bed

	

	# 2. create a grabix index of the file.

	#    creates simrep.chr1.bed.gbi

	grabix index simrep.chr1.bed.gz

	

	# 3. now, extract the 100th line in the file.

	grabix grab simrep.chr1.bed.gz 100

	chr1	401285	401444	trf	218

	

	# 4. extract the 100th through 110th lines in the file.

	grabix grab simrep.chr1.bed.gz 100 110

	chr1	401285	401444	trf	218

	chr1	401573	401748	trf	280

	chr1	404661	404707	trf	92

	chr1	406202	406274	trf	76

	chr1	406227	406286	trf	77

	chr1	406776	406819	trf	68

	chr1	409821	409866	trf	51

	chr1	409865	409900	trf	52

	chr1	421245	421285	trf	64

	chr1	422395	422435	trf	80

	chr1	422560	422588	trf	56

	

You can also use ``grabix`` to extract random lines from the file

	# extract 10 randome lines from the file using reservoir sampling

	grabix random simrep.chr1.bed.gz 10

    

Is a gzipped file bgzipped?

    grabix check simrep.chr1.bed.gz