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
all_gaps = hg19.gaps() # Returns gaps for all chromosomes
# Returns gaps for chromosome chrM
chrM_gaps = hg19.gaps(chromosomes=["chrM"])Getting filled regions
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()Release history Release notifications | RSS feed
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Hashes for ucsc_genomes_downloader-1.1.2.tar.gz
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