NOTE: this is work in progess. Here be dragons bugs. Potentially.
goontools processes GOON files.
GOON files?!
GOON (GenOme jsON) is a simple, flexible format that is easy to process, stream and extend. Its specification is the following:
- a GOON file is a line-delimited JSON (LDJSON) file
- every line encodes a datum of type Object
- every such object exposes a sequence name key with an associated String value and one or two position keys with associated integer values (strictly speaking of type Number with no fractional part)
...and that's it. Here's one valid GOON record, where CHR is the sequence name key and POS the (only) position key:
{"CHR": "chrX", "POS": 500017, "ALLELES": ["C", "T"]}
And in a different file you could have records with following structure: sequence name key chrom and position keys chromStart and chromEnd, whose values define an interval on the sequence.
{"chrom": "chr20", "chromStart": 0, "chromEnd": 500, "strand": "+"}
Back to goontools.
goontools provides a set of commands to manipulate GOON files.
In particular, following commands are currently implemented:
indexsortviewidxstatextract(experimental)pprint
Let's take a look at bed.ldj from the example directory:
# pretty-print first record
$ goontools pprint -n 1 bed.ldj
{
"chromEnd": 5,
"name": "name_0",
"score": 426,
"chromStart": 0,
"chrom": "10",
"strand": "-"
}
# sort and bgzip file:
$ goontools sort -s chrom -b chromStart bed.ldj > bed.srt.ldj
$ bgzip bed.srt.ldj
# positions are zero-based and "right-open" (non-inclusive end)
$ goontools index -0 -r -s chrom -b chromStart -e chromEnd bed.srt.ldj.gz
# check what we've indexed
$ goontools idxstat bed.srt.ldj.gz
SEQUENCE_NAME 1
SEQUENCE_NAME 10
SEQUENCE_NAME 11
SEQUENCE_NAME 3
SEQUENCE_NAME X
SEQUENCE_KEY chrom
START_KEY chromStart
END_KEY chromEnd
ZERO_BASED true
RIGHT_OPEN true
# get chromosome 1 records
$ goontools view bed.srt.ldj.gz 1
{"chromEnd": 11, "name": "name_6", "score": 711, "chromStart": 1, "chrom": "1", "strand": "+"}
{"chromEnd": 7, "name": "name_33", "score": 290, "chromStart": 2, "chrom": "1", "strand": "+"}
{"chromEnd": 4, "name": "name_49", "score": 923, "chromStart": 2, "chrom": "1", "strand": "-"}
{"chromEnd": 8, "name": "name_11", "score": 375, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 9, "name": "name_37", "score": 669, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 12, "name": "name_39", "score": 620, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_21", "score": 402, "chromStart": 5, "chrom": "1", "strand": "-"}
{"chromEnd": 7, "name": "name_44", "score": 725, "chromStart": 6, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_19", "score": 593, "chromStart": 7, "chrom": "1", "strand": "-"}
{"chromEnd": 17, "name": "name_5", "score": 392, "chromStart": 10, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_16", "score": 364, "chromStart": 10, "chrom": "1", "strand": "+"}
{"chromEnd": 19, "name": "name_32", "score": 371, "chromStart": 10, "chrom": "1", "strand": "-"}
{"chromEnd": 18, "name": "name_34", "score": 628, "chromStart": 10, "chrom": "1", "strand": "-"}
# get intersecting intervals
# by default `view` assumes position encoding from original file, i.e. 0-based, half-open here
$ goontools view bed.srt.ldj.gz 1:7-10
{"chromEnd": 11, "name": "name_6", "score": 711, "chromStart": 1, "chrom": "1", "strand": "+"}
{"chromEnd": 8, "name": "name_11", "score": 375, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 9, "name": "name_37", "score": 669, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 12, "name": "name_39", "score": 620, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_21", "score": 402, "chromStart": 5, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_19", "score": 593, "chromStart": 7, "chrom": "1", "strand": "-"}
# but we can also use a different encoding, e.g. pass a closed interval
$ goontools view -c bed.srt.ldj.gz 1:7-10
{"chromEnd": 11, "name": "name_6", "score": 711, "chromStart": 1, "chrom": "1", "strand": "+"}
{"chromEnd": 8, "name": "name_11", "score": 375, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 9, "name": "name_37", "score": 669, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 12, "name": "name_39", "score": 620, "chromStart": 4, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_21", "score": 402, "chromStart": 5, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_19", "score": 593, "chromStart": 7, "chrom": "1", "strand": "-"}
{"chromEnd": 17, "name": "name_5", "score": 392, "chromStart": 10, "chrom": "1", "strand": "-"}
{"chromEnd": 14, "name": "name_16", "score": 364, "chromStart": 10, "chrom": "1", "strand": "+"}
{"chromEnd": 19, "name": "name_32", "score": 371, "chromStart": 10, "chrom": "1", "strand": "-"}
{"chromEnd": 18, "name": "name_34", "score": 628, "chromStart": 10, "chrom": "1", "strand": "-"}goontools takes inspiration and quite a bit of actual
code from tabix[1] and samtools[2].
[1] http://samtools.sourceforge.net/
[2] http://bioinformatics.oxfordjournals.org/content/27/5/718.full
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