git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@61 60f365c0-8329-0410-b2a4-ec073aeeaa1d
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@ -15,6 +15,15 @@ void freememory(char **tab, int32_t num){
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}
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}
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/**
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* Check if a pattern match a string using mamberall libapat function
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* @param line array containing sequence information
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* @param pattern array containing patterns to test on the sequence
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* @param numpattern number of pattern in pattern array
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* @param error_max error rate allowed by the user
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*
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* @return int 1 if a pattern match, else 0
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**/
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int ispatternmatching(char **line, char **pattern, int32_t numpattern, int32_t error_max){
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int i;
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SeqPtr apatseq = NULL;
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@ -38,6 +47,11 @@ int ispatternmatching(char **line, char **pattern, int32_t numpattern, int32_t e
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return 0;
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}
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/**
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*returns the result on standard output
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* @param line array containing sequence information
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* @param i length of line
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**/
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void printline(char **line, int32_t i){
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int32_t k=0;
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for (k=0; k < i; k++)
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@ -99,36 +113,31 @@ static void ExitUsage(stat)
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int main(int argc, char **argv){
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int32_t carg = 0;
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int32_t r = 0; // number of restricted taxid
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int32_t g = 0; // number of ignored taxid
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int32_t v = 0;
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int32_t p = 0; // number of pattern
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int32_t r = 0; // number of restricted taxid
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int32_t g = 0; // number of ignored taxid
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int32_t v = 0; // stores if -v mode is active
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int32_t p = 0; // number of pattern
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int32_t i = 0;
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int32_t errflag = 0;
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int32_t error_max = 0;
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int32_t matchingresult = 0;
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int32_t error_max = 0; // stores the error rate allowed by the user
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int32_t matchingresult = 0; // stores number of matching result
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ecotaxonomy_t *taxonomy;
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ecotaxonomy_t *taxonomy; // stores the taxonomy
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char *database = NULL; // stores the database path (for taxonomy)
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int32_t *restricted_taxid = NULL; // stores the restricted taxid
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int32_t *ignored_taxid = NULL; // stores the ignored taxid
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char **pattern = NULL; // stores the regex pattern
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char *line[19] = {0}; // stores the line
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FILE *file = NULL;
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char *stream = ECOMALLOC(sizeof(char *)*10000,"error stream buffer allocation");
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int current_taxid;
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char *buffer;
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struct stat buf;
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FILE *file = NULL; // stores the data stream, stdin by default
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char *stream = ECOMALLOC(sizeof(char *)*10000,"error stream buffer allocation");
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char *buffer;
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// check stdin
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if (fstat(fileno(stdin),&buf) == 0)
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if ( (buf.st_dev) == 0)
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file = stdin;
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/**
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* Parse commande line options
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**/
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while ((carg = getopt(argc, argv, "f:d:i:r:e:vh")) != -1) {
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switch (carg) {
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@ -178,7 +187,7 @@ int main(int argc, char **argv){
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}
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/**
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* Get the leftover command line arguments back
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* Get the left-over command line arguments back
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* and check the pattern is not more than 32 character long
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*/
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pattern = ECOMALLOC(sizeof *pattern * (argc - optind), "Error in pattern allocation");
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@ -188,15 +197,26 @@ int main(int argc, char **argv){
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else
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{
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printf("# Sorry, ecogrep doesn't handle pattern longer than 32 characters.\
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\n# Please correct this one : %s\n",argv[optind]);
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\n# Please check it out : %s\n",argv[optind]);
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exit(0);
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}
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}
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/**
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* check standard input if no file name given in -f option
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**/
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if (file == NULL)
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{
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if (isatty(fileno(stdin)))
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errflag++;
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else
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file = stdin;
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}
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/**
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* try to get the database name from environment variable
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* if no database name specified in the -d option
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*/
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**/
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if (database == NULL)
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{
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database = getenv("ECOPCRDB");
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@ -205,12 +225,10 @@ int main(int argc, char **argv){
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}
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/**
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* check everything required is provided
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* check at leat one processing is asked
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* either patterns or taxid filters
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*/
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if ( !file ||
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!database ||
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(!p && restricted_taxid == NULL && ignored_taxid == NULL)
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)
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if ( !p && restricted_taxid == NULL && ignored_taxid == NULL )
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errflag++;
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if (errflag)
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@ -224,7 +242,7 @@ int main(int argc, char **argv){
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/**
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* Parse the stream
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*/
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while( fgets(stream, 10000, file) ){
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while( fgets(stream, 10000, file) != NULL ){
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if (stream[0]!= '#')
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{
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@ -232,6 +250,7 @@ int main(int argc, char **argv){
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buffer != NULL;
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i++, buffer = strtok(NULL,"|"))
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{
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printf("<EFBFBD><EFBFBD> %s\n",buffer);
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line[i] = strdup(buffer);
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}
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@ -254,7 +273,7 @@ int main(int argc, char **argv){
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continue;
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}
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else // v mode, invert ignore and restrict taxid
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else // v mode, invert ignore and restrict options
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{
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if ( (r > 0) && (eco_is_taxid_included( taxonomy,
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restricted_taxid,
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@ -280,12 +299,15 @@ int main(int argc, char **argv){
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printf("# %d matching result\n",matchingresult);
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/**
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* clean, close and free before leaving
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**/
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if ( file != stdin )
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fclose(file);
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freememory(line,i);
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freememory(pattern,p);
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ECOFREE(pattern,"Error in free pattern");
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ECOFREE(stream,"Error in free stream");
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return 0;
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}
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