Question: How to extract a particular region from a nucleotide contig?
The easiest (for me) would be:
from Bio import SeqIO rec = SeqIO.read('/path/to/file', 'format') # assuming only one sequence in the file prophage = rec[54501:90604] # write sequence out or do whatever analysis next.
You will need to double check the coordinates. Since python starts at 0, I think you may need to subtract 1 from each index.