ucsc-genomes-downloader 1.1.4

Python package to quickly download genomes from the UCSC.

Python package to quickly download and work with 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

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

Downloading selected chromosomes

from ucsc_genomes_downloader import Genome
hg19 = Genome("hg19", chromosomes=["chr1", "chr2"])

Getting gaps regions

The method return a DataFrame in bed-like format that contains the regions where only n or N nucleotides are present.

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

Getting filled regions

The method return a DataFrame in bed-like format that contains the regions where no unknown nucleotide is present, basically the complementary of the gaps method.

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

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()

Tasselizing bed files

Create a tasselization of a given size of a given bed-like pandas dataframe.

Available alignment are to the left, right or center.

from ucsc_genomes_downloader.utils import tasselize_bed
import pandas as pd

my_bed = pd.read_csv("path/to/my/file.bed", sep="\t")
tasselized = tasselize_bed(
    my_bed,
    window_size=200,
    alignment="left"
)