Awesome

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