cdot 0.2.9

Transcripts for HGVS libraries

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)

New in 0.2.8 - 2022-08-29

• Support for c_to_p - see changelog

Install

pip install cdot

Examples

Biocommons HGVS example:

import hgvs
from hgvs.assemblymapper import AssemblyMapper
from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider

hdp = RESTDataProvider()  # Uses API server at cdot.cc
# hdp = JSONDataProvider(["./cdot-0.2.8.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-0.2.8.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.

Q. Have you fully implemented the HGVS data provider interface?

We are working on it. The remaining functionality is:

Method	Status	Issue
get_tx_for_gene	Local JSON file only	REST API for get_tx_for_gene
get_tx_for_region	Local JSON file only	REST API for get_tx_for_region
get_acs_for_protein_seq	Not implemented	Implement get_acs_for_protein_seq
get_gene_info	Not implemented	Implement get_gene_info
get_similar_transcripts	Not implemented	Implement get_similar_transcripts