From 938bf7fa78e590bd625ffcec3264aeafbb8729f2 Mon Sep 17 00:00:00 2001 From: Dave Lawrence Date: Tue, 21 Mar 2023 15:32:04 +1030 Subject: [PATCH] Add wiki example code links, update changelog summary --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 978954b..699b3fa 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,9 @@ We currently support ~905k transcripts (vs ~141k in UTA v.20210129) See [changelog](https://github.com/SACGF/cdot/blob/main/CHANGELOG.md) -* 2023-02-23 - pyHGVS related bugfixes +2023-03-31: +* #31 - Fasta file Biocommons HGVS SeqFetcher implementation +* #38 - bugfix for Biocommons HGVS get_tx_for_region ## Install @@ -33,7 +35,7 @@ from hgvs.assemblymapper import AssemblyMapper from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider hdp = RESTDataProvider() # Uses API server at cdot.cc -# hdp = JSONDataProvider(["./cdot-0.2.10.refseq.grch37.json.gz"]) # Uses local JSON file +# hdp = JSONDataProvider(["./cdot-0.2.14.refseq.grch37.json.gz"]) # Uses local JSON file am = AssemblyMapper(hdp, assembly_name='GRCh37', @@ -44,6 +46,8 @@ var_c = hp.parse_hgvs_variant('NM_001637.3:c.1582G>A') am.c_to_g(var_c) ``` +[more Biocommons examples](https://github.com/SACGF/cdot/wiki/Biocommons-HGVS-example-code): + [PyHGVS](https://github.com/counsyl/hgvs) example: ``` @@ -53,10 +57,12 @@ from cdot.pyhgvs.pyhgvs_transcript import JSONPyHGVSTranscriptFactory, RESTPyHGV genome = FastaFile("/data/annotation/fasta/GCF_000001405.25_GRCh37.p13_genomic.fna.gz") factory = RESTPyHGVSTranscriptFactory() -# factory = JSONPyHGVSTranscriptFactory(["./cdot-0.2.12.refseq.grch37.json.gz"]) # Uses local JSON file +# 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](https://github.com/SACGF/cdot/wiki/PyHGVS-example-code): + ## Q. What's the performance like? * UTA public DB: 1-1.5 seconds / transcript