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cdot provides transcripts for the 2 most popular Python HGVS libraries.
It works by:
We currently support ~905k transcripts (vs ~141k in UTA v.20210129)
See changelog
2023-07-05:
2023-04-03:
pip install cdot
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)
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)
Download from GitHub releases - RefSeq (37/38) - 72M, Ensembl (37/38) 61M
Details on what the files contain here
Both projects have similar goals of providing transcripts for loading HGVS, but they approach it from different ways
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!
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.
FAQs
Transcripts for HGVS libraries
We found that cdot demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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