/usr/bin/windowmasker_2.2.22_adapter is in ncbi-blast+ 2.2.28-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 | #!/usr/bin/python
#
# Run this script without arguments to obtain usage informatioin.
#
import sys
import os
NAME_STR = 'windowmasker_2.2.22_adapter.py'
DESCR_STR = \
'old style to new style command line options\
converter for windowmasker'
VERSION_STR = '1.0'
HELP_STR = """
------------------------------------------------------------------------------
WINDOWMASKER COMMAND LINE OPTIONS CONVERTER
------------------------------------------------------------------------------
windowmasker_2.2.22_adapter.py takes old style command line for windowmasker,
converts it to the new format and runs the resulting command.
USAGE: windowmasker_2.2.22_adapter.py [--print-only] <wm_command> <options>
If '--print-only' flag is given as the first argument, then the resulting
command line is printed out, but windowmasker is not run.
wm_command is the path to windowmasker executable. It will be left unchanged
by the script.
------------------------------------------------------------------------------
"""
WM_NAME = 'windowmasker'
def title():
global NAME_STR, DESCR_STR, VERSION_STR
return NAME_STR + ': ' + DESCR_STR + '\nversion ' + VERSION_STR
def process( start_idx ):
old_wm_opt_info = {
'-h' : True,
'-help' : True,
'-xmlhelp' : True,
'-ustat' : False,
'-in' : False,
'-out' : False,
'-checkdup' : False,
'-window' : False,
'-t_extend' : False,
'-t_thres' : False,
'-t_high' : False,
'-t_low' : False,
'-set_t_high' : False,
'-set_t_low' : False,
'-infmt' : False,
'-parse_seqids' : False,
'-outfmt' : False,
'-sformat' : False,
'-mk_counts' : False,
'-convert' : False,
'-fa_list' : False,
'-mem' : False,
'-smem' : False,
'-unit' : False,
'-genome_size' : False,
'-dust' : False,
'-dust_level' : False,
'-exclude_ids' : False,
'-ids' : False,
'-text_match' : False,
'-use_ba' : False,
'-version' : True,
'-version-full' : True
}
tmpres = []
arg_pos = start_idx + 1
wm_mode = 'mask'
while True:
if arg_pos >= len( sys.argv ): break
arg = sys.argv[arg_pos]
if arg not in old_wm_opt_info.keys(): tmpres.append( arg )
else:
if arg == '-convert':
arg_pos += 1
if arg_pos < len( sys.argv ):
if sys.argv[arg_pos] in ['true', 'T', '1']:
tmpres.append( arg )
wm_mode = 'convert'
elif arg == '-mk_counts':
arg_pos += 1
if arg_pos < len( sys.argv ):
if sys.argv[arg_pos] in ['true', 'T', '1'] \
and wm_mode == 'mask':
tmpres.append( arg )
wm_mode = 'mk_counts'
elif old_wm_opt_info[arg]: tmpres.append( arg )
else:
tmpres.append( arg )
arg_pos += 1
if arg_pos < len( sys.argv ):
tmpres.append( sys.argv[arg_pos] )
arg_pos += 1
#print tmpres, wm_mode
excludes = {
'mk_counts' : [
'-outfmt',
'-ustat',
'-window',
'-t_thres',
'-t_extend',
'-set_t_low',
'-set_t_high',
'-dust',
'-dust_level',
'-convert'
],
'convert' : [
'-mk_counts',
'-ustat',
'-checkdup',
'-window',
'-t_extend',
'-t_thres',
'-t_high',
'-t_low',
'-set_t_high',
'-set_t_low',
'-infmt',
'-outfmt',
'-parse_seqids',
'-fa_list',
'-mem',
'-unit',
'-genome_size',
'-dust',
'-dust_level',
'-exclude_ids',
'-ids',
'-text_match',
'-use_ba'
],
'mask' : [
'-convert',
'-mk_counts',
'-checkdup',
'-fa_list',
'-mem',
'-unit',
'-genome_list',
'-sformat',
'-smem',
]
}
result = []
state = 'check'
for arg in tmpres:
if state == 'skip': state = 'check'
elif state == 'copy':
result.append( arg )
state = 'check'
elif arg in old_wm_opt_info.keys():
if arg in excludes[wm_mode]:
if not old_wm_opt_info[arg]: state = 'skip'
else:
result.append( arg )
if not old_wm_opt_info[arg]: state = 'copy'
else: result.append( arg )
return result
def main():
global HELP_STR
mode = 'exec'
if len( sys.argv ) <= 1:
print HELP_STR
return
else:
if sys.argv[1] == '--print-only':
mode = 'print'
if len( sys.argv ) <= 2:
print HELP_STR
return
else:
wm_name = sys.argv[2]
start_idx = 2
else:
wm_name = sys.argv[1]
start_idx = 1
new_args = process( start_idx )
result_str = wm_name + ' ' + ' '.join( new_args )
if mode == 'print': print result_str
else:
print 'running "' + result_str + '"'
os.system( result_str )
if __name__ == '__main__':
main()
|