I am trying to use bedtools and fetch sequences from a whole genome fasta file inside the script I get region coordinates as variables. For example:
chr_ = "chr1" start = 3000 end = 3402
I am not sure how to wrap my function, because the example provided by BedTool.sequence only uses coordinates in a string form.
Can you please help me to have something like this?
a = pybedtools.BedTool(chr_, start, end, from_variables=True)