Parse GFF file with

To install gffutils

pip install gffutils

Gffutils allow us to create sqlite db from gff file.

import gffutils
gffutils.create_db(filename, database_filename)

Then we can use the db for easily query data.

db = gffutils.FeatureDB(dbfn=database_filename)

For example, let’s say we need to work with gencode gff3 file look like:

##gff-version 3
#description: evidence-based annotation of the human genome (GRCh38), version 35 (Ensembl 101)
#provider: GENCODE
#format: gff3
#date: 2020-06-03
##sequence-region chr1 1 248956422
chr1 HAVANA gene 11869 14409 . + . ID=ENSG00000223972.5;gene_id=ENSG00000223972.5;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;level=2;hgnc_id=HGNC:37102;havana_gene=OTTHUMG00000000961.2
chr1 HAVANA transcript 11869 14409 . + . ID=ENST00000456328.2;Parent=ENSG00000223972.5;gene_id=ENSG00000223972.5;transcript_id=ENST00000456328.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=processed_transcript;transcript_name=DDX11L1-202;level=2;transcript_support_level=1;hgnc_id=HGNC:37102;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1

And we want to get “seqid”, “start”, “end”, “attributes” from the features type. Sample code for this is below.

Running this will show us the result


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A passionate automation engineer who strongly believes in “A man can do anything he wants if he puts in the work”.

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