https://github.com/gamcil/clinker/

https://cagecat.bioinformatics.nl/

https://pegaso.microbiologia.ull.es/clinker-server.php

1. code of extract_subregion.py

   import sys
   from Bio import SeqIO
   
   def extract_subregion(genbank_path, start, end, output_file):
       for record in SeqIO.parse(genbank_path, "genbank"):
           subregion = record[start:end]
           SeqIO.write(subregion, output_file, "genbank")
   
   if __name__ == "__main__":
       if len(sys.argv) < 5:
           print("Usage: python extract_subregion.py <GenBank file> <start> <end> <output file>")
           sys.exit(1)
   
       genbank_file = sys.argv[1]
       start = int(sys.argv[2])
       end = int(sys.argv[3])
       output_file = sys.argv[4]
   
       extract_subregion(genbank_file, start, end, output_file)

2. commands

   python3 extract_subregion.py HDRNA_01_K01_conservative_23197.current.gb 40434 55820 HDRNA_01_K01_sub.gb
   python3 extract_subregion.py HDRNA_03_K01_bold_bandage_26831.current.gb 2112517 2127744 HDRNA_03_K01_sub.gb
   python3 extract_subregion.py HDRNA_06_K01_conservative_27645.current_chr.gb 42053 58568 HDRNA_06_K01_sub.gb
   python3 extract_subregion.py HDRNA_07_K01_conservative_27169.current_chr.gb 37601 52993 HDRNA_07_K01_sub.gb
   python3 extract_subregion.py HDRNA_08_K01_conservative_32455.current_chr.gb 47084 68870 HDRNA_08_K01_sub.gb
   python3 extract_subregion.py HDRNA_12_K01_bold_37467.current_chr.gb 37586 52978 HDRNA_12_K01_sub.gb
   python3 extract_subregion.py HDRNA_16_K01_conservative_37834.current_chr.gb 37706 52877 HDRNA_16_K01_sub.gb
   python3 extract_subregion.py HDRNA_17_K01_conservative_37288.current_chr.gb 37118 52509 HDRNA_17_K01_sub.gb
   python3 extract_subregion.py HDRNA_19_K01_bold_37377.current_chr.gb 36267 51286 HDRNA_19_K01_sub.gb
   python3 extract_subregion.py HDRNA_20_K01_conservative_43457.current_chr.gb 37703 53095 HDRNA_20_K01_sub.gb
   
   clinker gbk_sub/*.gb -p plot.html --dont_set_origin -s session.json -o alignments.csv -dl "," -dc 4