Mimic legacy BLAST's formatdb to execute BLAST+ makeblastdb command: Legacy BLAST の formatdb のふりをして makeblastdb を実行する

gistfile1.py

#!/usr/bin/env python
# coding: utf-8
"""Mimic legacy BLAST's formatdb to execute BLAST+ makeblastdb command
"""
import argparse, os, sys

def main():
   sys.stderr.write('>>>>> %s\n' %(' '.join(sys.argv)))
   parser = argparse.ArgumentParser()
   simple_options_map = [
      ('i', 'in'),
      ('t', 'title'),
      ('l', 'logfile'),
      ('v', 'max_file_size'),
      ('n', 'out'),
      ('T', 'taxid_map'),
      ]
   
   flag_options_map = [
      ('o', 'hash_index'),
      ]

   special_options_map = [
      ('p', 'dbtype'),
      ('a', 'asn1_input'),
      ('b', 'asn1_binary'),
      ]

   undefined = ['s', 'L', 'F', 'B', 'V', 'e']

   for opt, dest in simple_options_map:
      parser.add_argument('-'+opt, dest=dest)

   for opt, dest in flag_options_map:
      parser.add_argument('-'+opt, dest=dest, nargs='?', const=True, default=False)

   #special options
   parser.add_argument('-e', dest='seq_entry_input')
   parser.add_argument('-p', dest='dbtype')
   parser.add_argument('-a', dest='asn1_input')
   parser.add_argument('-b', dest='asn1_binary')

   args = parser.parse_args()
   # selection of program
   program = 'makeblastdb'
   cmdline_args = [program]
   # simple argument conversion
   for opt, dest in simple_options_map:
      arg = getattr(args, dest, None)
      if not (arg==None):
         if False: # arg.split()>1:
            arg.strip('"').strip("'") # unquote
            arg = '"%s"' %arg # requote
         cmdline_args.extend(['-'+dest, arg])
   # flag conversion
   for opt, dest in flag_options_map:
      arg = getattr(args, dest, None)
      if arg==True:
         cmdline_args.append('-'+dest)
   # special conversion
   dbtype = getattr(args, 'dbtype')
   dbtype_val = 'prot'
   if dbtype=='F':
      dbtype_val = 'nucl'
   cmdline_args.extend(['-dbtype', dbtype_val])
   input_type='fasta'
   if getattr(args, 'asn1_input', None)=='T':
      input_type='asn1_txt'
   elif getattr(args, 'asn1_binary', None)=='T':
      input_type='asn1_bin'
   if input_type != 'fasta':
      cmdline_args.extend(['-input_type', input_type])
   sys.stderr.write('>>>>> %s\n' %(' '.join(cmdline_args)))
   os.execvp(program, cmdline_args)

if __name__=='__main__':
   main()