mehari-data

Reproducible data builds for mehari.

This repository contains scripts to build the transcript protobuf files for meharib based on SACGF/cdot.

Resulting Files

The following explains the content and compatibility.

• mehari-data v0.2.1
  • compatible to: mehari v0.4.1..
  • grch37 data file: mehari-data-txs-grch37-0.2.1.bin.zst
    • cdot: v0.2.14
    • genome release: GRCh37.p13
    • VEP/ENSEMBL equivalent: r105
    • RefSeq assembly: GCF_000001405.25
  • grch38 data: mehari-data-txs-grch38-0.2.1.bin.zst
    • cdot: v0.2.14
    • genome release: GRCh38.p13
    • VEP/ENSEMBL equivalent: r109
    • RefSeq assembly: GCF_000001405.39

So, for example:

• mehari-data-txs-grch37-0.2.1.bin.zst is compatible to the mehari software v0.4.1 and above;
• it was created from the cdot transcripts v0.2.14;
• these were built for GRCh37.p13 based on the VEP/ENSEMBL Release r105
• and the transcripts from the RefSeq assembly GCF_000001405.25.

New builds of mehari-data will be considered when

• the new mehari software version changes protobuf schema, OR
• a new cdot has a new release corresponding to a VEP release, OR
• bugs are found and make a new release necessary.

Generally, only the data for the latest mehari protobuf schema is created.

Utility Files

As RefSeq does not contain transcripts for mitochondrial genes, we graft the ENSEMBL transcripts over.

# python src/cdot_extract_chrmt.py \
      /tmp/cdot-0.2.24.ensembl.Homo_sapiens.GRCh37.87.gff3.json.gz \
  > data/cdot-0.2.24.ensembl.chrMT.grch37.gff3.json

# python src/cdot_extract_chrmt.py \
      /tmp/cdot-0.2.24.ensembl.Homo_sapiens.GRCh38.111.gff3.json.gz \
  > data/cdot-0.2.24.ensembl.chrMT.grch38.gff3.json