Mimic legacy blast's blastall to execute BLAST+ commands: Legacy blastall のふりをして BLAST+ コマンドを実行する

blastall

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

def main():
   sys.stderr.write('>>>>> %s\n' %(' '.join(sys.argv)))   
   parser = argparse.ArgumentParser()
   parser.add_argument('-p', dest='program', required=True)
   simple_options_map = [
      ('d', 'db'), 
      ('i', 'query'),
      ('e', 'evalue'),
      ('m', 'outfmt'),
      ('o', 'out'),
      ('G', 'gapopen'),
      ('E', 'gapextend'),
      ('q', 'penalty'),
      ('r', 'reward'),
      ('v', 'num_descriptions'),
      ('b', 'num_alignments'),
      ('f', 'threshold'),
      ('Q', 'query_genetic_code'),
      ('D', 'db_gen_code'),
      ('a', 'num_threads'),
      ('M', 'matrix'),
      ('W', 'word_size'),
      ('z', 'dbsize'),
      ('Y', 'searchsp'),
      ('S', 'strand'),
      ('l', 'gilist'),
      ('y', 'xdrop_ungap'),
      ('Z', 'xdrop_gap_final'),
      ('X', 'xdrop_gap'),
      ('L', 'query_loc'),
      ('A', 'window_size'),
      ('t', 'max_intron_length'),
      ('C', 'comp_based_stats'),
      ('s', 'use_sw_tback'),
      ]
   
   flag_options_map = [
      ('I', 'show_gis'),
      ('J', 'parse_deflines'),
      ('T', 'html'),
      ('U', 'lcase_masking'),
      ('V', 'legacy'),
      ]

   special_options_map = [
      ('F', 'dust_seg'),
      ('g', 'ungapped'),
      ('n', 'megablast'),
      ]

   undefined_options = ['O', 'K', 'P', 'R', 'w', 'B']

   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('-F', dest='dust_seg')
   parser.add_argument('-g', dest='gapped')
   parser.add_argument('-n', dest='megablast')

   args = parser.parse_args()
   # selection of program
   program = args.program
   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
   dust_seg = getattr(args, 'dust_seg')
   if not dust_seg==None:
      sw = '-seg'
      if program=='blastn':
         sw = '-dust'
      val = 'no'
      if dust_seg=='F':
         val = 'yes'
      cmdline_args.extend([sw, val])
   gapped = getattr(args, 'gapped', None)
   if not gapped==None:
      if gapped=='T':
         cmdline_args.extend(['-ungapped', 'no'])
      else:
         cmdline_args.extend(['-ungapped', 'yes'])
   megablast = getattr(args, 'megablast', None)
   if not megablast==None:
      if megablast=='T':
         cmdline_args.extend(['-task', 'megablast'])
   sys.stderr.write('>>>>> %s\n' %(' '.join(cmdline_args)))
   os.execvp(program, cmdline_args)

if __name__=='__main__':
   main()