pybedtools.helpers.get_chromsizes_from_ucsc¶
- pybedtools.helpers.get_chromsizes_from_ucsc(genome, saveas=None, mysql='mysql', fetchchromsizes='fetchChromSizes', timeout=None, host_url='genome-mysql.cse.ucsc.edu')[source]¶
Download chrom size info for genome from UCSC and returns the dictionary.
- Parameters:
- genomestr
Name of the genome assembly (e.g., “hg38”)
- saveasstr
Filename to save output to. Dictionary will still be returned.
- mysql, fetchchromsizesstr
Paths to MySQL and fetchChromSizes.
- timeoutfloat
How long to wait for a response; mostly used for testing.
- host_urlstr
URL of UCSC mirror MySQL server.