obitools/ecopcr
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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@58 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-12 08:38:22 +00:00
parent cdc0375356
commit 7fbd940ba2
1 changed files with 22 additions and 21 deletions
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43
src/ecogrep.c
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@ -3,6 +3,8 @@
#include <string.h> #include <string.h>
#include <stdlib.h> #include <stdlib.h>
#include <getopt.h> #include <getopt.h>
#include <stdlib.h>
#include <sys/stat.h>
#define VERSION "0.1" #define VERSION "0.1"
@ -23,7 +25,6 @@ int ispatternmatching(char **line, char **pattern, int32_t numpattern, int32_t e
sscanf(line[4],"%d",&seq->taxid); sscanf(line[4],"%d",&seq->taxid);
seq->AC = strdup(line[0]); seq->AC = strdup(line[0]);
//seq->DE = strdup(line[]);
seq->SQ = strdup(line[18]); seq->SQ = strdup(line[18]);
seq->SQ_length = strlen(line[18]); seq->SQ_length = strlen(line[18]);
@ -66,9 +67,9 @@ static void PrintHelp()
PP " -r : [R]estrict taxomic id\n\n"); PP " -r : [R]estrict taxomic id\n\n");
PP " -v : in[V]ert the sense of matching, to select non-matching lines.\n"); PP " -v : in[V]ert the sense of matching, to select non-matching lines.\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP " Pattern : oligonucleotide pattern\n");; PP " Pattern : oligonucleotide pattern\n");
PP "------------------------------------------\n\n"); PP "------------------------------------------\n\n");
PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki"); PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n");
PP "------------------------------------------\n\n"); PP "------------------------------------------\n\n");
} }
@ -109,26 +110,31 @@ int main(int argc, char **argv){
ecotaxonomy_t *taxonomy; ecotaxonomy_t *taxonomy;
char *filename = NULL; // stores the datafile name
char *database = NULL; // stores the database path (for taxonomy) char *database = NULL; // stores the database path (for taxonomy)
int32_t *restricted_taxid = NULL; // stores the restricted taxid int32_t *restricted_taxid = NULL; // stores the restricted taxid
int32_t *ignored_taxid = NULL; // stores the ignored taxid int32_t *ignored_taxid = NULL; // stores the ignored taxid
char **pattern = NULL; // stores the regex pattern char **pattern = NULL; // stores the regex pattern
char *line[19] = {0}; // stores the line char *line[19] = {0}; // stores the line
FILE *file = NULL; FILE *file = NULL;
char *stream = ECOMALLOC(sizeof(char *)*10000,"error stream buffer allocation"); char *stream = ECOMALLOC(sizeof(char *)*10000,"error stream buffer allocation");
int current_taxid; int current_taxid;
char *buffer; char *buffer;
struct stat buf;
// check stdin
if (fstat(fileno(stdin),&buf) == 0)
if ( (buf.st_dev) == 0)
file = stdin;
while ((carg = getopt(argc, argv, "f:d:i:r:e:vh")) != -1) { while ((carg = getopt(argc, argv, "f:d:i:r:e:vh")) != -1) {
switch (carg) { switch (carg) {
case 'f': case 'f':
filename = ECOMALLOC(strlen(optarg)+1, if ( (file = fopen(optarg, "r")) == NULL)
"Error on filename allocation"); errflag++;
strcpy(filename,optarg);
break; break;
case 'd': case 'd':
@ -201,22 +207,14 @@ int main(int argc, char **argv){
/** /**
* check everything required is provided * check everything required is provided
*/ */
if (!filename || if ( !file ||
!database || !database ||
(!p && restricted_taxid == NULL && ignored_taxid == NULL)) (!p && restricted_taxid == NULL && ignored_taxid == NULL)
)
errflag++; errflag++;
if (errflag) if (errflag)
ExitUsage(errflag); ExitUsage(errflag);
/**
* Open the ecoPCR file
*/
if (filename)
{
if( (file = fopen(filename, "r")) == NULL)
ECOERROR(ECO_IO_ERROR,"Cannot open the file !");
}
/** /**
* Get the taxonomy back * Get the taxonomy back
@ -282,6 +280,9 @@ int main(int argc, char **argv){
printf("# %d matching result\n",matchingresult); printf("# %d matching result\n",matchingresult);
if ( file != stdin )
fclose(file);
freememory(line,i); freememory(line,i);
freememory(pattern,p); freememory(pattern,p);
ECOFREE(pattern,"Error in free pattern"); ECOFREE(pattern,"Error in free pattern");