Computational biology is 90% text formatting and ID cross-referencing!
-- discouraged graduate students everywhere
tag is a free open-source software package for analyzing genome annotation data.
# Compute number of exons per gene
import tag
reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
for gene in tag.select.features(reader, type='gene'):
exons = [feat for feat in gene if feat.type == exon]
print('num exons:', len(exons))To install the most recent stable release execute pip install tag from your terminal.
Full installation instructions and project documentation are available at https://tag.readthedocs.io.