git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@114 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
345
src/ecofind.c
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345
src/ecofind.c
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#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
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**/
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static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
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{
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char* rankname;
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char* classname;
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char* matchedname=taxon->name;
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classname="scientific name";
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if (name)
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{
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classname=name->classname;
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matchedname=name->name;
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}
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rankname= taxonomy->ranks->label[taxon->rank];
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printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s\n",
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taxon->taxid,
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rankname,
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matchedname,
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classname,
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taxon->name);
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}
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/**
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* display header before printing any result
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**/
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static void printheader(void)
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{
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printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s\n#\n",
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"taxonomy id",
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"taxonomy rank",
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"name",
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"class name",
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"scientific name");
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}
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/**
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* display son's list for given taxon
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**/
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static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname)
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{
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int32_t i;
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ecotx_t *current_taxon;
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for ( i = 0, current_taxon = taxonomy->taxons->taxon;
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i < taxonomy->taxons->count;
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i++, current_taxon++)
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{
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if (taxon->taxid == current_taxon->parent->taxid)
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{
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if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[current_taxon->rank]))
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{
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printresult(current_taxon, NULL, taxonomy);
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(*count)++;
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}
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get_son(taxonomy,current_taxon,count,rankname);
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}
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}
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}
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/**
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* display list of rank filter option (-l option)
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**/
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static void listfilteroptions(ecorankidx_t *ranks)
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{
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int32_t i;
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printf("#\n");
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for ( i=0;
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i < ranks->count;
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i++)
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{
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printf("# %s \n",ranks->label[i]);
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}
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printf("#\n");
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}
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/* ---------------------------------------- */
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/* get back on given taxid taxonomic parent */
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/* and display it */
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/* ---------------------------------------- */
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void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname)
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{
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ecotx_t *next_parent;
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int32_t c = 0;
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next_parent = eco_findtaxonbytaxid(taxonomy, taxid);
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printheader();
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printresult(next_parent, NULL,taxonomy);
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while ( strcmp(next_parent->name, "root") )
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{
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next_parent = next_parent->parent;
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if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[next_parent->rank]))
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{
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printresult(next_parent, NULL,taxonomy);
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c++;
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}
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}
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printf("# %d parent(s) found\n#\n",c);
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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 database] [-h] [-l] [-r taxonomic rank] [-p taxid] [-s taxid] <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 taxonomic and rank and\n");
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PP " taxonomy id for given regular expression patterns\n\n");
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PP "usage: ecofind [options] <patterns>\n");
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PP "------------------------------------------\n");
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PP "options:\n");
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PP "-a : [A]ll enable the search on all alternative names and not only scientific names.\n\n");
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PP "-d : [D]atabase 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 database radical without any extension.\n\n");
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PP "-h : [H]elp - print <this> help\n\n");
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PP "-l : [L]ist all taxonomic rank available for -r option\n\n");
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PP "-p : [P]arents : specifiying this option displays all parental tree's information for the given taxid.\n\n");
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PP "-r : [R]estrict to given taxonomic rank\n\n");
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PP "-s : [S]ons: specifiying this option displays all subtree's information for the given taxid.\n\n");
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PP "arguments:\n");
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PP "<taxon> name pattern bearing regular expressions\n\n");
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PP "------------------------------------------\n");
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PP " http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
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PP "------------------------------------------\n\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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int32_t alternative = 0;
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char *prefix = NULL;
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ecotaxonomy_t *taxonomy;
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econame_t *name;
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int32_t name_count;
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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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int32_t uptree = 0;
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int32_t subtree = 0;
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char *rankname = NULL;
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int32_t rankfilter = 1;
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int32_t list = 0;
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ecotx_t *subtree_parent;
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int32_t count_son = 0;
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while ((carg = getopt(argc, argv, "had:p:s:r:l")) != -1) {
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switch (carg) {
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case 's': /* path to the database */
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sscanf(optarg,"%d",&subtree);
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break;
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case 'r': /* rank filter */
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rankname = ECOMALLOC(strlen(optarg),"allocation rankname");
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strcpy(rankname,optarg);
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rankfilter = 0;
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break;
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case 'd': /* path to the database */
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prefix = ECOMALLOC(strlen(optarg),"allocation prefix");
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strcpy(prefix,optarg);
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break;
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case 'l': /* list rank filter options */
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list = 1;
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break;
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case 'a': /* allow alternative names */
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alternative = 1;
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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 'p': /* taxid */
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sscanf(optarg,"%d",&uptree);
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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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if ((argc - optind) < 1)
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errflag++;
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if (prefix == NULL)
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{
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prefix = getenv("ECOPCRDB");
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if (prefix == NULL)
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errflag++;
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}
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if (errflag && !uptree && !rankname && !subtree && !list)
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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,1);
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tax_count = taxonomy->taxons->count;
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name_count = taxonomy->names->count;
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/* ---------------------------------------- */
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/* list -r option possibility */
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/* ---------------------------------------- */
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if (list)
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{
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listfilteroptions(taxonomy->ranks);
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return 0;
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}
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/* ---------------------------------------- */
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/* display taxid parent if -t option */
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/* specified in command line */
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/* ---------------------------------------- */
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if (uptree)
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{
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gettaxidparents(uptree,taxonomy,rankname);
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return 0;
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}
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/* ---------------------------------------- */
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/* display taxid sons if -s option */
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/* specified in command line */
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/* ---------------------------------------- */
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if (subtree)
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{
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printheader();
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subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
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printresult(subtree_parent, NULL,taxonomy);
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get_son(taxonomy, subtree_parent,&count_son,rankname);
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printf("# %d son(s) found\n#\n",count_son);
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return 0;
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}
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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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printheader();
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for (j=0,name=taxonomy->names->names;
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j < name_count;
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name++,j++)
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{
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if(rankname)
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rankfilter = !(strcmp(rankname,taxonomy->ranks->label[name->taxon->rank]));
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re_match = regexec (&re_preg, name->name, 0, NULL, 0);
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if (!re_match && (alternative || name->is_scientificname) && rankfilter)
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{
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printresult(name->taxon,name,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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