use samtools faidx to index and retrieve those coordinates

grep -v -E '^>|^$' input.fasta | tr -d '\n' | cut -c 54501-90604 | fold -w 60

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.