This file is indexed.

/usr/bin/promer is in mummer 3.23+dfsg-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
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
#!/usr/bin/perl

#-------------------------------------------------------------------------------
#   Programmer: Adam M Phillippy, The Institute for Genomic Research
#         File: promer
#         Date: 04 / 09 / 03
#
#        Usage:
#    promer  [options]  <Reference>  <Query>
#
#                Try 'promer -h' for more information.
#
#      Purpose: To create alignments between two multi-FASTA inputs by using
#              the MUMmer matching and clustering algorithms.
#
#-------------------------------------------------------------------------------

use lib "/usr/share/perl5/";
use Foundation;
use File::Spec::Functions;
use strict;

my $AUX_BIN_DIR = "/usr/lib/mummer";
my $BIN_DIR = "/usr/bin";
my $SCRIPT_DIR = "/usr/share/perl5/";



my $VERSION_INFO = q~
PROmer (PROtein MUMmer) version 3.07
    ~;



my $HELP_INFO = q~
  USAGE: promer  [options]  <Reference>  <Query>

  DESCRIPTION:
    promer generates amino acid alignments between two mutli-FASTA DNA input
    files. The out.delta output file lists the distance between insertions
    and deletions that produce maximal scoring alignments between each
    sequence. The show-* utilities know how to read this format. The DNA
    input is translated into all 6 reading frames in order to generate the
    output, but the output coordinates reference the original DNA input.

  MANDATORY:
    Reference       Set the input reference multi-FASTA DNA file
    Query           Set the input query multi-FASTA DNA file

  OPTIONS:
    --mum           Use anchor matches that are unique in both the reference
                    and query
    --mumcand       Same as --mumreference
    --mumreference  Use anchor matches that are unique in in the reference
                    but not necessarily unique in the query (default behavior)
    --maxmatch      Use all anchor matches regardless of their uniqueness

    -b|breaklen     Set the distance an alignment extension will attempt to
                    extend poor scoring regions before giving up, measured in
                    amino acids (default 60)
    -c|mincluster   Sets the minimum length of a cluster of matches, measured in
                    amino acids (default 20)
    --[no]delta     Toggle the creation of the delta file (default --delta)
    --depend        Print the dependency information and exit
    -d|diagfactor   Set the clustering diagonal difference separation factor
                    (default .11)
    --[no]extend    Toggle the cluster extension step (default --extend)
    -g|maxgap       Set the maximum gap between two adjacent matches in a
                    cluster, measured in amino acids (default 30)
    -h
    --help          Display help information and exit.
    -l|minmatch     Set the minimum length of a single match, measured in amino
                    acids (default 6)
    -m|masklen      Set the maximum bookend masking lenth, measured in amino
                    acids (default 8)
    -o
    --coords        Automatically generate the original PROmer1.1 ".coords"
                    output file using the "show-coords" program
    --[no]optimize  Toggle alignment score optimization, i.e. if an alignment
                    extension reaches the end of a sequence, it will backtrack
                    to optimize the alignment score instead of terminating the
                    alignment at the end of the sequence (default --optimize)

    -p|prefix       Set the prefix of the output files (default "out")
    -V
    --version       Display the version information and exit
    -x|matrix       Set the alignment matrix number to 1 [BLOSUM 45], 2 [BLOSUM
                    62] or 3 [BLOSUM 80] (default 2)
    ~;


my $USAGE_INFO = q~
  USAGE: promer  [options]  <Reference>  <Query>
    ~;


my @DEPEND_INFO =
    (
     "$BIN_DIR/mummer",
     "$BIN_DIR/mgaps",
     "$BIN_DIR/show-coords",
     "$AUX_BIN_DIR/postpro",
     "$AUX_BIN_DIR/prepro",
     "$SCRIPT_DIR/Foundation.pm"
     );


my %DEFAULT_PARAMETERS =
    (
     "OUTPUT_PREFIX"     =>   "out",      # prefix for all output files
     "MATCH_ALGORITHM"   =>   "-mumreference", # match finding algo switch
     "MIN_MATCH"         =>   "6",        # minimum match size (aminos)
     "MAX_GAP"           =>   "30",       # maximum gap between matches (aminos)
     "MIN_CLUSTER"       =>   "20",       # minimum cluster size (aminos)
     "DIAG_FACTOR"       =>   ".11",      # diagonal difference fraction
     "BREAK_LEN"         =>   "60",       # extension break length
     "BLOSUM_NUMBER"     =>   "2",        # options are 1,2,3 (BLOSUM 45,62,80)
     "MASKING_LENGTH"    =>   "8",        # set bookend masking length
     "POST_SWITCHES"     =>   ""          # switches for the post processing
     );


sub main ( )
{
    my $tigr;             # TIGR::Foundation object
    my @err;              # Error variable
    
    my $ref_file;         # path of the reference input file
    my $qry_file;         # path of the query input file

    #-- The command line options for the various programs
    my $pfx = $DEFAULT_PARAMETERS { "OUTPUT_PREFIX" };
    my $algo = $DEFAULT_PARAMETERS { "MATCH_ALGORITHM" };
    my $size = $DEFAULT_PARAMETERS { "MIN_MATCH" };
    my $gap = $DEFAULT_PARAMETERS { "MAX_GAP" };
    my $clus = $DEFAULT_PARAMETERS { "MIN_CLUSTER" };
    my $diff = $DEFAULT_PARAMETERS { "DIAG_FACTOR" };
    my $blen = $DEFAULT_PARAMETERS { "BREAK_LEN" };
    my $blsm = $DEFAULT_PARAMETERS { "BLOSUM_NUMBER" };
    my $mask = $DEFAULT_PARAMETERS { "MASKING_LENGTH" };
    my $psw = $DEFAULT_PARAMETERS { "POST_SWITCHES" };

    my $maxmatch;         # matching algorithm switches
    my $mumreference;
    my $mum;
    my $extend = 1;       # if true, extend clusters
    my $delta = 1;        # if true, create the delta file
    my $optimize = 1;     # if true, optimize alignment scores

    my $generate_coords;

    #-- Initialize TIGR::Foundation
    $tigr = new TIGR::Foundation;
    if ( !defined ($tigr) ) {
	print (STDERR "ERROR: TIGR::Foundation could not be initialized");
	exit (1);
    }
    
    #-- Set help and usage information
    $tigr->setHelpInfo ($HELP_INFO);
    $tigr->setUsageInfo ($USAGE_INFO);
    $tigr->setVersionInfo ($VERSION_INFO);
    $tigr->addDependInfo (@DEPEND_INFO);

    #-- Get command line parameters
    $err[0] = $tigr->TIGR_GetOptions
	(
         "maxmatch" => \$maxmatch,
	 "mumcand" => \$mumreference,
         "mumreference" => \$mumreference,
         "mum" => \$mum,
	 "b|breaklen=i" => \$blen,
	 "c|mincluster=i" => \$clus,
	 "delta!" => \$delta,
	 "d|diagfactor=f" => \$diff,
	 "extend!" => \$extend,
	 "g|maxgap=i" => \$gap,
	 "l|minmatch=i" => \$size,
	 "m|masklen=i" => \$mask,
	 "o|coords"   => \$generate_coords,
	 "optimize!" => \$optimize,
	 "p|prefix=s" => \$pfx,
	 "x|matrix=i" => \$blsm
	 );

    #-- Check if the parsing was successful
    if ( $err[0] == 0  ||  $#ARGV != 1 ) {
	$tigr->printUsageInfo( );
	print (STDERR "Try '$0 -h' for more information.\n");
	exit (1);
    }

    $ref_file = File::Spec->rel2abs ($ARGV[0]);
    $qry_file = File::Spec->rel2abs ($ARGV[1]);
    
    #-- Set up the program parameters
    if ( ! $extend ) {
	$psw .= "-e ";
    }
    if ( ! $delta ) {
	$psw .= "-d ";
    }
    if ( ! $optimize ) {
	$psw .= "-t ";
    }

    undef (@err);
    $err[0] = 0;
    if ( $mum ) {
	$err[0] ++;
	$algo = "-mum";
    }
    if ( $mumreference ) {
	$err[0] ++;
	$algo = "-mumreference";
    }
    if ( $maxmatch ) {
	$err[0] ++;
	$algo = "-maxmatch";
    }
    if ( $err[0] > 1 ) {
	$tigr->printUsageInfo( );
	print (STDERR "ERROR: Multiple matching algorithms selected\n");
	print (STDERR "Try '$0 -h' for more information.\n");
	exit (1);
    }

    #-- Set up the program path names
    my $algo_path = "$BIN_DIR/mummer";
    my $mgaps_path = "$BIN_DIR/mgaps";
    my $prepro_path = "$AUX_BIN_DIR/prepro";
    my $postpro_path = "$AUX_BIN_DIR/postpro";
    my $showcoords_path = "$BIN_DIR/show-coords";
		     
    #-- Check that the files needed are all there and readable/writable
    {
	undef (@err);
	if ( !$tigr->isExecutableFile ($algo_path) ) {
	    push (@err, $algo_path);
	}
	
	if ( !$tigr->isExecutableFile ($mgaps_path) ) {
	    push (@err, $mgaps_path);
	}
	
	if ( !$tigr->isExecutableFile ($prepro_path) ) {
	    push (@err, $prepro_path);
	}
	
	if ( !$tigr->isExecutableFile ($postpro_path) ) {
	    push (@err, $postpro_path);
	}
	
	if ( !$tigr->isReadableFile ($ref_file) ) {
	    push (@err, $ref_file);
	}
	
	if ( !$tigr->isReadableFile ($qry_file) ) {
	    push (@err, $qry_file);
	}
	
	if ( !$tigr->isCreatableFile ("$pfx.aaref") ) {
	    if ( !$tigr->isWritableFile ("$pfx.aaref") ) {
		push (@err, "$pfx.aaref");
	    }
	}

	if ( !$tigr->isCreatableFile ("$pfx.aaqry") ) {
	    if ( !$tigr->isWritableFile ("$pfx.aaqry") ) {
		push (@err, "$pfx.aaqry");
	    }
	}
	
	if ( !$tigr->isCreatableFile ("$pfx.mgaps") ) {
	    if ( !$tigr->isWritableFile ("$pfx.mgaps") ) {
		push (@err, "$pfx.mgaps");
	    }
	}
	
	if ( !$tigr->isCreatableFile ("$pfx.delta") ) {
	    if ( !$tigr->isWritableFile ("$pfx.delta") ) {
		push (@err, "$pfx.delta");
	    }
	}

	if ( $generate_coords ) {
	    if ( !$tigr->isExecutableFile ($showcoords_path) ) {
		push (@err, $showcoords_path);
	    }
	    if ( !$tigr->isCreatableFile ("$pfx.coords") ) {
		if ( !$tigr->isWritableFile ("$pfx.coords") ) {
		    push (@err, "$pfx.coords");
		}
	    }
	}
    
	#-- If 1 or more files could not be processed, terminate script
	if ( $#err >= 0 ) {
	    $tigr->logError
		("ERROR: The following critical files could not be used", 1);
	    while ( $#err >= 0 ) {
		$tigr->logError (pop(@err), 1);
	    }
	    $tigr->logError
		("Check your paths and file permissions and try again", 1);
	    $tigr->bail( );
	}
    }
    

    #-- Run prepro -r and -q and assert return value is zero
    print (STDERR "1: PREPARING DATA\n");
    $err[0] = $tigr->runCommand
	("$prepro_path -m $mask -r $ref_file > $pfx.aaref");

    if ( $err[0] != 0 ) {
	$tigr->bail
	    ("ERROR: prepro -r returned non-zero\n");
    }

    $err[0] = $tigr->runCommand
	("$prepro_path -m $mask -q $qry_file > $pfx.aaqry");

    if ( $err[0] != 0 ) {
	$tigr->bail ("ERROR: prepro -q returned non-zero\n");
    }


    #-- Run mummer | mgaps and assert return value is zero
    print (STDERR "2,3: RUNNING mummer AND CREATING CLUSTERS\n");
    open(ALGO_PIPE, "$algo_path $algo -l $size $pfx.aaref $pfx.aaqry |")
	or $tigr->bail ("ERROR: could not open $algo_path output pipe $!");
    open(CLUS_PIPE, "| $mgaps_path -l $clus -s $gap -f $diff > $pfx.mgaps")
	or $tigr->bail ("ERROR: could not open $mgaps_path input pipe $!");
    while ( <ALGO_PIPE> ) {
	print CLUS_PIPE
	or $tigr->bail ("ERROR: could not write to $mgaps_path pipe $!");
    }
    $err[0] = close(ALGO_PIPE);
    $err[1] = close(CLUS_PIPE);

    if ( $err[0] == 0  ||  $err[1] == 0 ) {
	$tigr->bail ("ERROR: mummer and/or mgaps returned non-zero\n");
    }


    #-- Run postpro and assert return value is zero
    print (STDERR "4: FINISHING DATA\n");
    $err[0] = $tigr->runCommand
	("$postpro_path $psw -x $blsm -b $blen ".
	 "$ref_file $qry_file $pfx < $pfx.mgaps");

    if ( $err[0] != 0 ) {
	$tigr->bail ("ERROR: postpro returned non-zero\n");
    }

    #-- If the -o flag was set, run show-coords using PROmer1.1 settings
    if ( $generate_coords ) {
	print (STDERR "5: GENERATING COORDS FILE\n");
	$err[0] = $tigr->runCommand
	    ("$showcoords_path -r $pfx.delta > $pfx.coords");
	
	if ( $err[0] != 0 ) {
	    $tigr->bail ("ERROR: show-coords returned non-zero\n");
	}
    }
 
    #-- Remove the temporary output
    $err[0] = unlink ("$pfx.aaref", "$pfx.aaqry", "$pfx.mgaps");
 
    if ( $err[0] != 3 ) {
 	$tigr->logError ("WARNING: there was a problem deleting".
			 " the temporary output files", 1);
    }
 
    #-- Return success
    return (0);
}

exit ( main ( ) );

#-- END OF SCRIPT