ucsc-genomes-downloader 1.1.0

Python package to quickly download genomes from the UCSC.

Python package to quickly download genomes from the UCSC.

How do I install this package?

As usual, just download it using pip:

pip install ucsc_genomes_downloader

Tests Coverage

Since some software handling coverages sometime get slightly different results, here’s three of them:

Usage examples

Simply instanziate a new genome

Create a new Genome object for the given genome hg19.

from ucsc_genomes_downloader import Genome
hg19 = Genome("hg19")

Downloading lazily a genome’s chromosome

Download mitochondrial genome “chromosome” for the genome “sacCer3” (downloads the chromosomes only when required).

from ucsc_genomes_downloader import Genome
sacCer3 = Genome("sacCer3")
chrM = sacCer3["chrM"] # Downloads and returns mitochondrial genome

Downloading eagerly a genome

Download all genome’s chromosomes immediately.

from ucsc_genomes_downloader import Genome
sacCer3 = Genome("sacCer3", lazy_download=False)

Loading eagerly a genome

Load (and downloads if necessary) into RAM all the genome’s chromosomes immediately.

from ucsc_genomes_downloader import Genome
sacCer3 = Genome("sacCer3", lazy_load=False)

Testing if a genome is cached

if hg19.is_cached():
    print("Genome is cached!")

Getting gaps regions

If you need a bed file containing the regions with gaps you can use:

all_gaps = hg19.gaps() # Returns gaps for all chromosomes
chrM_gaps = hg19.gaps(chromosomes=["chrM"]) # Returns gaps for chromosome chrM

Getting filled regions

If you need a bed file containing the filled regions you can use:

all_filled = hg19.filled() # Returns filled for all chromosomes
chrM_filled = hg19.filled(chromosomes=["chrM"]) # Returns filled for chromosome chrM

Getting BED sequences

Given a BED-like pandas dataframe, you can get the corresponding sequences as follows:

my_bed = pd.read_csv("path/to/my.bed", sep="\t")
sequences = hg19.bed_to_sequence(my_bed)

Removing genome’s cache

hg19.delete()

Utilities

Retrieving a list of the available genomes

You can get a complete list of the genomes available from the UCSC website with the following method:

from ucsc_genomes_downloader import get_available_genomes
all_genomes = get_available_genomes()