cdot

cdot provides transcripts for the 2 most popular Python HGVS libraries.

It works by:

Converting RefSeq/Ensembl GTFs to JSON
Providing loaders for the HGVS libraries, via JSON.gz files, or REST API via cdot_rest)

We currently support ~893k transcripts (vs ~141k in UTA v.20210129)

Install

pip install cdot

Examples

Biocommons HGVS example:

from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider

hdp = RESTDataProvider()  # Uses API server at cdot.cc
# hdp = JSONDataProvider(["./cdot-0.2.6.refseq.grch38.json.gz"])  # Uses local JSON file

am = AssemblyMapper(hdp,
                    assembly_name='GRCh37',
                    alt_aln_method='splign', replace_reference=True)

hp = hgvs.parser.Parser()
var_c = hp.parse_hgvs_variant('NM_001637.3:c.1582G>A')
am.c_to_g(var_c)

PyHGVS example:

from cdot.pyhgvs.pyhgvs_transcript import JSONPyHGVSTranscriptFactory, RESTPyHGVSTranscriptFactory

factory = RESTPyHGVSTranscriptFactory()
# factory = JSONPyHGVSTranscriptFactory(["./cdot-0.2.6.refseq.grch38.json.gz"])  # Uses local JSON file
pyhgvs.parse_hgvs_name(hgvs_c, genome, get_transcript=factory.get_transcript_grch37)

Q. What's the performance like?

UTA public DB: 1-1.5 seconds / transcript
cdot REST service: 10/second
cdot JSON.gz: 500-1k/second

Q. Where can I download the JSON.gz files?

RefSeq 37+38 - 70Mb Ensembl 37+38 - 53Mb

See also Download JSON.gz files if you only want individual builds.

Q. How does this compare to Universal Transcript Archive?

Both projects have similar goals of providing transcripts for loading HGVS, but they approach it from different ways

UTA aligns sequences, then stores coordinates in an SQL database.
cdot convert existing Ensembl/RefSeq GTFs into JSON

See wiki for more details

Q. How do you store transcripts in JSON?

See wiki page for the format.

We think a standard for JSON gene/transcript information would be a great thing, and am keen to collaborate to make it happen!

Q. What does cdot stand for?

cdot, pronounced "see dot" stands for Complete Dict of Transcripts

This was developed for the Australian Genomics Shariant project, due to the need to load historical HGVS from lab archives.

Akazhiel/cdot