# How to use variables while calling pybedtools

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.

a = pybedtools.BedTool(chr_, start, end, from_variables=True)


You have to take your variables and make them into a single string variable.

for example:

chr_ = "chr1"
start = 3000
end = 3402
as_str = ' '.join([chr_, str(start), str(end)])
# or
as_str2 = "{} {} {}".format(chr_, start, end)


Once you have the string built you can use the example in the bedTool docs.

a = BedTool(as_str, from_string=True)

• If you like an answer please accept it so future users know it worked. – Bioathlete May 31 '18 at 17:58