5
votes
Accepted
Is there a JSON-based genomic feature format?
JVCF is a JSON schema for describing genetic variants. BioJSON is a JSON schema for multiple sequence alignments. The output of mygene.info's gene annotation web service is JSON-formatted.
You might ...
- 3,045
1
vote
Accepted
GenomicRanges: get nearest neighbor distances for random genes using a for loop
Is it because rand.gr has not been initialised, so when you ask to set rand.gr[i] it can't because there isn't one yet?
If you set i to a value (e.g. 1), and run the lines inside your loop, which of ...
- 1,012
1
vote
Is there a JSON-based genomic feature format?
I've written a Python library called PyReference which converts a GTF / GFF (RefSeq and Ensembl) into a gzipped JSON file.
You can just use this if you like but there's also a Python wrapper around ...
- 153
1
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Is there a JSON-based genomic feature format?
BioJS has capacity to read and write GFF as streams, it might have something of interest such as this: https://github.com/biojs-io/biojs-io-gff
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