build_gene_transcript_db

URI NOTES

Create a environment variable called MYSQL_PWD with the passoword of your MYSQL user:

export MYSQL_PWD=your_mysql_password

Create a database to link gene names (HUGO) with the following genome resources: GENCODE/Ensembl, RefSeq, MANE and LRG.

TODO

• Add RefSeq isoforms whose CDS do not match at 100% with GENCODE/Ensembl
• Check disparity between transcript versions (i.e ENST00001.X)

Installation

This code has been successfully tested to run in python 3.8. You can check your python3 version by prompting: python3 -V. Also, you will need pip3 as a package manager.

It is advisable to use a virtual environment to build the project: python3 -m virtualenv mypython

1. Get CrossMap

CrossMap handles coordinate conversions between genome versions. To install it:

pip3 install CrossMap

You can check that CrossMap is installed properly by prompting on the terminal: CrossMap.py

2. Install python3 dependencies

pip3 install -r requeriments.txt

Basic usage:

Run the code with this command. You may want to introduce an output directory using parameter --output_dir.

python3 gene_isoform_models.py --output_dir <output_directory>

Upon execution, the following database will be generated:

GENE_SYMBOL	ENST_ID	ENSP_ID	REFSEQ_CDS_COMPLETE	REFSEQ_PROTEIN_ID	MANE_SELECT	MANE_PLUS_CLINICAL	LRG_ID	LRG_TRANSCRIPT
SCN5A	ENST00000423572	ENSP00000398266.2	NM_000335.5	NP_000326.2	NM_000335.5	.	LRG_289	t2
SCN5A	ENST00000327956	ENSP00000333674.6		NP_000326.2	.	.	.	.
SCN5A	ENST00000414099	ENSP00000398962.2	NM_001099405.2	NP_000326.2	.	.	.	.
SCN5A	ENST00000333535	ENSP00000328968.4	NM_198056.3	NP_000326.2	.	.	LRG_289	t1
SCN5A	ENST00000413689	ENSP00000410257.1	NM_001099404.2	NP_000326.2	.	NM_001099404.2	LRG_289	t3
SCN5A	ENST00000450102	ENSP00000403355.2	NM_001160161.2	NP_000326.2	.	.	.	.
SCN5A	ENST00000449557	ENSP00000413996.2		NP_000326.2	.	.	.	.
SCN5A	ENST00000455624	ENSP00000399524.2	NM_001160160.2	NP_000326.2	.	.	.	.

All gff3 files that populate the database will be downloaded within the following folder schema:

GENE_TRANSCRIPT_DATABASE
│
└───MANE
│   └───1.0
│       │───GRCh37
│             MANE.GRCh37.v1.0.ensembl_genomic.gff.gz
│       │───GRCh38
│             MANE.GRCh38.v1.0.ensembl_genomic.gff.gz
│
└───GENCODE
│   └───39
│       │───GRCh37
│             gencode.v39lift37.annotation.gff3.gz
│       │───GRCh38
│             gencode.v39.annotation.gff3.gz
│
└───RefSeq
│   └───102
│       │───GRCh37
│             GRCh37_latest_genomic.gff.gz
│       │───GRCh38
│             GRCh38_latest_genomic.gff.gz
│
└───LRG
│   └───1.10
│       list_LRGs_transcripts_xrefs.txt