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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@48 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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Eric Coissac
2007-06-08 12:53:41 +00:00
parent 6b28897ff5
commit 255ab0c670
1 changed files with 70 additions and 69 deletions
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139
src/ecopcr.c
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@ -8,8 +8,8 @@
#define VERSION "0.1" #define VERSION "0.1"
/* ----------------------------------------------- */ /* ----------------------------------------------- */
/* printout help */ /* ----------------------------------------------- */ /* printout help */
/* ----------------------------------------------- */
#define PP fprintf(stdout, #define PP fprintf(stdout,
static void PrintHelp() static void PrintHelp()
@ -21,56 +21,56 @@ static void PrintHelp()
PP "usage: ecoPCR [options] datafile\n"); PP "usage: ecoPCR [options] datafile\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "options:\n"); PP "options:\n");
PP "-1 : [FIRST] oligonucleotide for direct strand\n\n"); PP "-1 : [FIRST] oligonucleotide for direct strand\n\n");
PP "-2 : [SECOND] oligonucleotide for reverse strand\n\n"); PP "-2 : [SECOND] oligonucleotide for reverse strand\n\n");
PP "-e : [E]rror \n"); PP "-e : [E]rror \n");
PP " : max error allowed by oligonucleotide\n\n"); PP " : max error allowed by oligonucleotide\n\n");
PP "-h : [H]elp - print <this> help\n\n"); PP "-h : [H]elp - print <this> help\n\n");
PP "-i : [I]gnore the given taxonomy id.\n"); PP "-i : [I]gnore the given taxonomy id.\n");
PP " taxonomy id are available using the ecofind program.\n"); PP " taxonomy id are available using the ecofind program.\n");
PP " see its help typing ecofind -h for more information.\n"); PP " see its help typing ecofind -h for more information.\n");
PP "-k : [K]ingdom mode\n"); PP "-k : [K]ingdom mode\n");
PP " set the kingdom mode\n"); PP " set the kingdom mode\n");
PP " super kingdom mode by default.\n\n"); PP " super kingdom mode by default.\n\n");
PP "-l : minimum [L]ength\n"); PP "-l : minimum [L]ength\n");
PP " define the minimum amplication length. \n\n"); PP " define the minimum amplication length. \n\n");
PP "-L : maximum [L]ength\n"); PP "-L : maximum [L]ength\n");
PP " define the maximum amplicationlength. \n\n"); PP " define the maximum amplicationlength. \n\n");
PP "-r : [R]estricts the search to the given taxonomy id.\n"); PP "-r : [R]estricts the search to the given taxonomy id.\n");
PP " taxonomy id are available using the ecofind program.\n"); PP " taxonomy id are available using the ecofind program.\n");
PP " see its help typing ecofind -h for more information.\n"); PP " see its help typing ecofind -h for more information.\n");
PP "\n"); PP "\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "datafile : to match the expected format, the database\n"); PP "datafile : to match the expected format, the database\n");
PP "has to be formated first by the ecoPCRFormat.py program located.\n"); PP "has to be formated first by the ecoPCRFormat.py program located.\n");
PP "in the tools directory.\n"); PP "in the tools directory.\n");
PP "ecoPCRFormat.py creates three file types :"); PP "ecoPCRFormat.py creates three file types :");
PP " .sdx : contains the sequences\n"); PP " .sdx : contains the sequences\n");
PP " .tdx : contains information concerning the taxonomy\n"); PP " .tdx : contains information concerning the taxonomy\n");
PP " .rdx : contains the taxonomy rank\n\n"); PP " .rdx : contains the taxonomy rank\n\n");
PP "ecoPCR needs all the file type. As a result, you have to write the\n"); PP "ecoPCR needs all the file type. As a result, you have to write the\n");
PP "datafile radical without any extension. For example /database/gbmam\n"); PP "datafile radical without any extension. For example /database/gbmam\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "Table result description : \n"); PP "Table result description : \n");
PP "column 1 : accession number\n"); PP "column 1 : accession number\n");
PP "column 2 : sequence length\n"); PP "column 2 : sequence length\n");
PP "column 3 : taxonomic id\n"); PP "column 3 : taxonomic id\n");
PP "column 4 : rank\n"); PP "column 4 : rank\n");
PP "column 5 : species taxonomic id\n"); PP "column 5 : species taxonomic id\n");
PP "column 6 : scientific name\n"); PP "column 6 : scientific name\n");
PP "column 7 : genus taxonomic id\n"); PP "column 7 : genus taxonomic id\n");
PP "column 8 : genus name\n"); PP "column 8 : genus name\n");
PP "column 9 : family taxonomic id\n"); PP "column 9 : family taxonomic id\n");
PP "column 10 : family name\n"); PP "column 10 : family name\n");
PP "column 11 : super kingdom taxonomic id\n"); PP "column 11 : super kingdom taxonomic id\n");
PP "column 11 : super kingdom name\n"); PP "column 11 : super kingdom name\n");
PP "column 13 : strand (direct or reverse)\n"); PP "column 13 : strand (direct or reverse)\n");
PP "column 14 : first oligonucleotide\n"); PP "column 14 : first oligonucleotide\n");
PP "column 15 : number of errors for the first strand\n"); PP "column 15 : number of errors for the first strand\n");
PP "column 16 : second oligonucleotide\n"); PP "column 16 : second oligonucleotide\n");
PP "column 17 : number of errors for the second strand\n"); PP "column 17 : number of errors for the second strand\n");
PP "column 18 : amplification length\n"); PP "column 18 : amplification length\n");
PP "column 19 : sequence description\n"); PP "column 19 : sequence description\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP "\n"); PP "\n");
@ -87,7 +87,7 @@ static void PrintHelp()
static void ExitUsage(stat) static void ExitUsage(stat)
int stat; int stat;
{ {
PP "usage: ecoPCR [-1 oligo1] [-2 oligo2] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-k] datafile\n"); PP "usage: ecoPCR [-d database] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-k] oligo1 oligo2\n");
PP "type \"ecoPCR -h\" for help\n"); PP "type \"ecoPCR -h\" for help\n");
if (stat) if (stat)
@ -270,7 +270,7 @@ int main(int argc, char **argv)
int32_t errflag=0; int32_t errflag=0;
char kingdom_mode=0; char kingdom_mode=0;
char *prefix; char *prefix = NULL;
int32_t checkedSequence = 0; int32_t checkedSequence = 0;
int32_t positiveSequence= 0; int32_t positiveSequence= 0;
@ -300,23 +300,15 @@ int main(int argc, char **argv)
int32_t g=0; int32_t g=0;
while ((carg = getopt(argc, argv, "h1:2:l:L:e:i:r:k")) != -1) { while ((carg = getopt(argc, argv, "hd:l:L:e:i:r:k")) != -1) {
switch (carg) { switch (carg) {
/* -------------------- */ /* -------------------- */
case '1': /* first primer */ case 'd': /* database name */
/* -------------------- */ /* -------------------- */
oligo1 = ECOMALLOC(strlen(optarg)+1, prefix = ECOMALLOC(strlen(optarg)+1,
"Error on oligo 1 allocation"); "Error on prefix allocation");
strcpy(oligo1,optarg); strcpy(prefix,optarg);
break;
/* -------------------- */
case '2': /* second primer */
/* -------------------- */
oligo2 = ECOMALLOC(strlen(optarg)+1,
"Error on oligo 1 allocation");
strcpy(oligo2,optarg);
break; break;
/* -------------------- */ /* -------------------- */
@ -378,17 +370,26 @@ int main(int argc, char **argv)
/** /**
* check the path to the database is given as last argument * check the path to the database is given as last argument
*/ */
if ((argc -= optind) != 1) if ((argc -= optind) == 2)
errflag++; {
oligo1 = ECOMALLOC(strlen(argv[optind])+1,
"Error on oligo1 allocation");
strcpy(oligo1,argv[optind]);
optind++;
oligo2 = ECOMALLOC(strlen(argv[optind])+1,
"Error on oligo1 allocation");
strcpy(oligo2,argv[optind]);
}
else
errflag++;
if (!oligo1 || !oligo2) if (!oligo1 || !oligo2)
errflag++; errflag++;
if (errflag) if (errflag)
ExitUsage(errflag); ExitUsage(errflag);
prefix = argv[optind];
o1 = buildPattern(oligo1,error_max); o1 = buildPattern(oligo1,error_max);
o2 = buildPattern(oligo2,error_max); o2 = buildPattern(oligo2,error_max);
@ -423,10 +424,10 @@ int main(int argc, char **argv)
amplifiatCount = 0; amplifiatCount = 0;
while(seq) while(seq)
{ {
checkedSequence++; checkedSequence++;
/** /**
* check if current sequence should be ignored * check if current sequence should be included
**/ **/
if ( (r == 0) || if ( (r == 0) ||
(eco_is_taxid_included(taxonomy, (eco_is_taxid_included(taxonomy,