cdot 0.2.15

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 ~905k transcripts (vs ~141k in UTA v.20210129)

New

See changelog

2023-04-03:

• #41 - Support for T2T CHM13v2.0

2023-03-31:

• #31 - Fasta file Biocommons HGVS SeqFetcher implementation
• #38 - bugfix for Biocommons HGVS get_tx_for_region

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-0.2.14.refseq.grch37.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)

more Biocommons examples:

PyHGVS example:

import pyhgvs
from pysam.libcfaidx import FastaFile
from cdot.pyhgvs.pyhgvs_transcript import JSONPyHGVSTranscriptFactory, RESTPyHGVSTranscriptFactory

genome = FastaFile("/data/annotation/fasta/GCF_000001405.25_GRCh37.p13_genomic.fna.gz")
factory = RESTPyHGVSTranscriptFactory()
# factory = JSONPyHGVSTranscriptFactory(["./cdot-0.2.14.refseq.grch37.json.gz"])  # Uses local JSON file
pyhgvs.parse_hgvs_name('NM_001637.3:c.1582G>A', genome, get_transcript=factory.get_transcript_grch37)

more PyHGVS examples:

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?

Download from GitHub releases - RefSeq (37/38) - 72M, Ensembl (37/38) 61M

Details on what the files contain here

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.