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Announcing cdot - a way to load lots of transcripts fast #62

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davmlaw opened this issue Feb 3, 2022 · 0 comments
Open

Announcing cdot - a way to load lots of transcripts fast #62

davmlaw opened this issue Feb 3, 2022 · 0 comments

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@davmlaw
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davmlaw commented Feb 3, 2022

I've made a Python package that provides ~800k transcripts (both RefSeq and Ensembl) for PyHGVS

https://github.com/SACGF/cdot

You can either download a JSON.gz file, or use a REST service. To use it:

from cdot.pyhgvs.pyhgvs_transcript import JSONPyHGVSTranscriptFactory, RESTPyHGVSTranscriptFactory

factory = RESTPyHGVSTranscriptFactory()
# factory = JSONPyHGVSTranscriptFactory(["./cdot-0.2.1.refseq.grch38.json.gz"])  # Uses local JSON file
pyhgvs.parse_hgvs_name(hgvs_c, genome, get_transcript=factory.get_transcript_grch37)
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