160 lines
3.8 KiB
C
160 lines
3.8 KiB
C
#include "libecoPCR/ecoPCR.h"
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#include <regex.h>
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#include <string.h>
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#include <stdlib.h>
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#include <getopt.h>
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#include <stdio.h>
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#define VERSION "0.1"
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/**
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* display the result in sdtout
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**/
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static void printresult(ecotx_t *taxon,ecotaxonomy_t *taxonomy){
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char* rankname;
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rankname= taxonomy->ranks->label[taxon->rank];
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printf("%10d \t| %15s \t|\t %s\n",
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taxon->taxid,
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rankname,
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taxon->name);
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}
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/**
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* printout usage and exit
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**/
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#define PP fprintf(stderr,
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static void ExitUsage(stat)
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int stat;
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{
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PP "usage: ecofind [-d datafile] [-h] <taxon name pattern> ... \n");
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PP "type \"ecofind -h\" for help\n");
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if (stat)
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exit(stat);
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}
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#undef PP
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/**
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* printout help
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**/
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#define PP fprintf(stdout,
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static void PrintHelp()
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{
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PP "------------------------------------------\n");
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PP " ecofind Version %s\n", VERSION);
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PP "------------------------------------------\n");
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PP "synopsis : searching for scientific name, taxonomic\n");
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PP " rank and taxonomy id for given regular\n");
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PP " expression patterns\n");
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PP "usage: ecofind [options]\n");
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PP "------------------------------------------\n");
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PP "options:\n");
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PP "-d : [D]atafile containing the taxonomy\n");
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PP " to match the expected format, the database\n");
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PP " has to be formated first by the ecoPCRFormat.py\n");
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PP " program located in the tools directory.\n");
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PP " Write the datafile radical without any extension.\n\n");
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PP "-h : [H]elp - print <this> help\n\n");
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PP "<taxon> name pattern bearing regular expressions\n\n");
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PP "------------------------------------------\n");
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}
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/* ----------------------------------------------- */
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#define PATTERN_NUMBER 10
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#define PATTERN_LENGHT 40
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#define RESULT_LENGTH 100
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int main(int argc, char **argv)
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{
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int32_t carg = 0;
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int32_t nummatch = 0;
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int32_t k,j = 0;
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int32_t errflag = 0;
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int32_t tax_count = 0;
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char *prefix = NULL;
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ecotx_t *taxon = NULL;
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ecotaxonomy_t *taxonomy;
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int re_error;
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int re_match;
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regex_t re_preg;
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while ((carg = getopt(argc, argv, "hd:")) != -1) {
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switch (carg) {
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case 'd': /* path to the database */
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prefix = optarg;
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break;
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case 'h': /* display help */
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PrintHelp();
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exit(0);
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break;
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case '?': /* bad option */
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errflag++;
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}
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}
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/**
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* check the path to the database is given as last argument
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**/
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if ((argc - optind) < 1)
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errflag++;
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if (errflag)
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ExitUsage(errflag);
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/**
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* load taxonomy using libecoPCR functions
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**/
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printf("# \n# opening %s database\n",prefix);
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taxonomy = read_taxonomy(prefix);
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tax_count = taxonomy->taxons->count;
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printf("# %d taxons\n", tax_count);
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/**
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* parse taxonomy
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**/
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for (k=optind;k<argc;k++)
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{
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printf("#\n# searching for '%s' pattern\n",argv[k]);
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re_error = regcomp (&re_preg, argv[k], REG_NOSUB | REG_EXTENDED | REG_ICASE);
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if (re_error)
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{
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fprintf(stderr,"# misformed pattern '%s'\n",argv[k]);
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exit(1);
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}
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nummatch=0;
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printf("# taxonomy id \t|\t taxonomy rank \t|\t scientific name\n#\n");
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for (j=0,taxon=taxonomy->taxons->taxon;
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j < tax_count;
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taxon++,j++)
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{
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re_match = regexec (&re_preg, taxon->name, 0, NULL, 0);
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if (re_match == 0)
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{
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printresult(taxon,taxonomy);
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nummatch++;
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}
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}
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printf("# %d records found \n",nummatch);
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regfree(&re_preg);
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}
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return 0;
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}
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