cdot 0.1.1

Transcripts for HGVS libraries

cdot

cdot is used to load transcripts for the 2 most popular Python HGVS libraries.

It works by:

• Converting RefSeq and Ensembl GTFs into a JSON format
• Providing loaders from that JSON format (or a REST service)

We currently support 788k transcripts, 5.5x as many as Universal Transcript Archive

Examples

Biocommons HGVS example:

from cdot.hgvs.dataproviders import JSONDataProvider, RESTDataProvider

hp = JSONDataProvider({"GRCh37": "./cdot_220119.grch38.json.gz")  # Uses local JSON file
# hp = RESTDataProvider()  # Uses API server at cdot.cc

am = AssemblyMapper(hp,
                    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:

# TODO

Philosophical differences from Universal Transcript Archive

cdot aims to be as simple as possible: convert existing Ensembl/RefSeq GTFs into JSON format

Universal transcript archive is an excellent and ambitious project that:

• Performs its own mapping of transcript sequences to reference genomes
• Stores the transcript version data (exons etc) in a SQL database

This has some advantages, namely that you can resolve a GRCh37 coordinate for a transcript which was never officially released for that build.

However the complexity causes a few downsides:

• Alignments may not exactly match those in official Ensembl/RefSeq releases
• Local install requires a PostgreSQL installation
• Internet hosted UTA is a PostgreSQL server, so requires client Postgres libraries, is inaccessible behind firewalls. They have been planning on building a REST server since 2014
• High complexity manual process for releases means they do not support Ensembl and take a while to make RefSeq releases.