Attachment #93119 for bug #142269

View | Details | Raw Unified | Return to bug 142269
Collapse All | Expand All





#include <ostream>
#include <unistd.h>  // getopt
#include <stdlib.h> // getenv
#include "MCFgen.hpp"  // die, tostring
#include "MCFbio.hpp"  // count_residues
#include "args.hpp"

of sequence motifs in a FASTA-like format described below. Any non-alphabetic\n\
characters in the sequences are ignored, and any alphabetic characters except A,\n\
C, G, T (uppercase or lowercase) are converted to 'n' and excluded from matching\n\
motifs. The motif file should look like this:\n\
\n\
>TATA\n\
0 0 0 10\n\

In addition to the two required inputs, there several options for modifying\n\
Clover's behavior:\n\
 -h  Help: print documentation. You already know this one.\n\
 -f  alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n\
 -r  Number of randomized/control raw scores to calculate for comparison with\n\
     each target raw score.\n\
 -t  P-value threshold: only print results for motifs whose P-values don't\n\

";

  const string usage =
    "Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]\n"
    "\nYou should set the CLOVER_MOTIF_FILE environmental variable\n"
    "or specify the path to a motif file as clover option\n\n"
    "Options:\n"
    "-h  help: print documentation\n"
    "-f  alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n"
    "-r  number of randomizations (" + tostring(shuffles) + ")\n"
    "-t  P-value threshold (" + tostring(pthresh) + ")\n"
    "-u  motif score threshold (" + tostring(hit_thresh) + ")\n"

    "-s  seed for random number generator (" + tostring(random_seed) + ")\n"
    ;

  char *cptr;
  if ((cptr = getenv( "CLOVER_MOTIF_FILE" )) != NULL ) {
     mat_file = cptr;
  }
  int c;

  while ((c = getopt(argc, argv, "hr:t:u:ndmlvp:s:")) != -1)
    switch (c) {
    case 'h':
      cout << doc << endl;
      exit(0);
    case 'f':
      	mat_file = optarg;
	break;
    case 'r':
      shuffles = atoi(optarg);
      break;

      mcf::die("\n" + usage);  // "invalid option" message is printed by getopt
    }

  if (optind + 2 > argc)  // there should be 2 more non-option arguments
    mcf::die("Error: motif and sequence files required\n\n" + usage);

  if (optind + 1 > argc)  // there should be 2 more non-option arguments
    mcf::die("*** Error: sequence file required\n\n" + usage);

  mat_file = argv[optind++];
  seq_file = argv[optind++];

  while (optind < argc)

Return to bug 142269

Lines 5-11 Link Here

(-)args.cpp.new (-20 / +6 lines)
5		5
6	#include <ostream>	6	#include <ostream>
7	#include <unistd.h> // getopt	7	#include <unistd.h> // getopt
8	#include <stdlib.h> // getenv
9	#include "MCFgen.hpp" // die, tostring	8	#include "MCFgen.hpp" // die, tostring
10	#include "MCFbio.hpp" // count_residues	9	#include "MCFbio.hpp" // count_residues
11	#include "args.hpp"	10	#include "args.hpp"
Lines 58-64 Link Here
58	of sequence motifs in a FASTA-like format described below. Any non-alphabetic\n\	57	of sequence motifs in a FASTA-like format described below. Any non-alphabetic\n\
59	characters in the sequences are ignored, and any alphabetic characters except A,\n\	58	characters in the sequences are ignored, and any alphabetic characters except A,\n\
60	C, G, T (uppercase or lowercase) are converted to 'n' and excluded from matching\n\	59	C, G, T (uppercase or lowercase) are converted to 'n' and excluded from matching\n\
61	motifs. The motif file, specified either in the CLOVER_MOTIF_FILE variable or as clover option, should look like this:\n\	60	motifs. The motif file should look like this:\n\
62	\n\	61	\n\
63	>TATA\n\	62	>TATA\n\
64	0 0 0 10\n\	63	0 0 0 10\n\
Lines 130-136 Link Here
130	In addition to the two required inputs, there several options for modifying\n\	129	In addition to the two required inputs, there several options for modifying\n\
131	Clover's behavior:\n\	130	Clover's behavior:\n\
132	-h Help: print documentation. You already know this one.\n\	131	-h Help: print documentation. You already know this one.\n\
133	-f alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n\
134	-r Number of randomized/control raw scores to calculate for comparison with\n\	132	-r Number of randomized/control raw scores to calculate for comparison with\n\
135	each target raw score.\n\	133	each target raw score.\n\
136	-t P-value threshold: only print results for motifs whose P-values don't\n\	134	-t P-value threshold: only print results for motifs whose P-values don't\n\
Lines 162-173 Link Here
162	";	160	";
163		161
164	const string usage =	162	const string usage =
165	"Usage summary: clover [options] myseqs.fa [BGfiles]\n"	163	"Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]\n"
166	"\nYou should set the CLOVER_MOTIF_FILE environmental variable\n"
167	"or specify the path to a motif file as clover option\n\n"
168	"Options:\n"	164	"Options:\n"
169	"-h help: print documentation\n"	165	"-h help: print documentation\n"
170	"-f alternative motif file (overrides CLOVER_MOTIF_FILE variable)\n"
171	"-r number of randomizations (" + tostring(shuffles) + ")\n"	166	"-r number of randomizations (" + tostring(shuffles) + ")\n"
172	"-t P-value threshold (" + tostring(pthresh) + ")\n"	167	"-t P-value threshold (" + tostring(pthresh) + ")\n"
173	"-u motif score threshold (" + tostring(hit_thresh) + ")\n"	168	"-u motif score threshold (" + tostring(hit_thresh) + ")\n"
Lines 180-199 Link Here
180	"-s seed for random number generator (" + tostring(random_seed) + ")\n"	175	"-s seed for random number generator (" + tostring(random_seed) + ")\n"
181	;	176	;
182		177
183	char *cptr;
184	if ((cptr = getenv( "CLOVER_MOTIF_FILE" )) != NULL ) {
185	mat_file = cptr;
186	}
187	int c;	178	int c;
188		179
189	while ((c = getopt(argc, argv, "hf:r:t:u:ndmlvp:s:")) != -1)	180	while ((c = getopt(argc, argv, "hr:t:u:ndmlvp:s:")) != -1)
190	switch (c) {	181	switch (c) {
191	case 'h':	182	case 'h':
192	cout << doc << endl;	183	cout << doc << endl;
193	exit(0);	184	exit(0);
194	case 'f':
195	mat_file = optarg;
196	break;
197	case 'r':	185	case 'r':
198	shuffles = atoi(optarg);	186	shuffles = atoi(optarg);
199	break;	187	break;
Lines 228-239 Link Here
228	mcf::die("\n" + usage); // "invalid option" message is printed by getopt	216	mcf::die("\n" + usage); // "invalid option" message is printed by getopt
229	}	217	}
230		218
231	if (mat_file.empty())	219	if (optind + 2 > argc) // there should be 2 more non-option arguments
232	mcf::die("*** Error: Motif file not specified\n\n" + usage);	220	mcf::die("Error: motif and sequence files required\n\n" + usage);
233
234	if (optind + 1 > argc) // there should be 2 more non-option arguments
235	mcf::die("*** Error: sequence file required\n\n" + usage);
236		221
		222	mat_file = argv[optind++];
237	seq_file = argv[optind++];	223	seq_file = argv[optind++];
238		224
239	while (optind < argc)	225	while (optind < argc)