Python package to quickly download genomes from the UCSC.
Project description
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_downloaderTests 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.utils 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"
)Expand bed files regions
Expand a given dataframe in bed-like format using selected alignment.
Available alignment are to the left, right or center.
from ucsc_genomes_downloader.utils import expand_bed_regions
import pandas as pd
my_bed = pd.read_csv("path/to/my/file.bed", sep="\t")
expanded = expand_bed_regions(
my_bed,
window_size=1000,
alignment="left"
)Release history Release notifications | RSS feed
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