32 Fetching gene tracks as PyRanges
PyRanges can fetch data from UCSC, GENCODE, Ensembl and the GWAS catalog through
the pyranges_db add-on package. It can be installed with pip install pyranges_db.
Each database contains at least two methods, namely genes and genomes. UCSC and Ensembl also has the method chromosome_sizes.
The genes-methods all take a boolean flag head. If true, it only fetches a few thousand rows of data.
(The below commands are intentionally commented out for now since they require several dependencies that I do not want to require to build the book.)
print("Intentionally commented out! Try the commands yourself instead.")
# import pyranges_db as pr_db
#
# genomes = pr_db.ucsc.genomes()
#
# print(genomes.head())
#
# chr_sizes = pr_db.ucsc.chromosome_sizes("hg38")
#
# print(chr_sizes)
#
# genes = pr_db.ucsc.genes("hg38", head=True)
#
# print(genes)
#
# gwas = pr_db.gwas_catalog.gwas_catalog(nrows=500)
#
# print(gwas)## Intentionally commented out! Try the commands yourself instead.