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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@69 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-20 07:37:27 +00:00
parent 388fe75522
commit d8696f0566
1 changed files with 161 additions and 30 deletions
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185
src/ecofind.c
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@ -7,20 +7,87 @@
#define VERSION "0.1" #define VERSION "0.1"
/** /**
* display the result in sdtout * display the result
**/ **/
static void printresult(ecotx_t *taxon,ecotaxonomy_t *taxonomy) static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
{ {
char* rankname; char* rankname;
char* classname;
char* matchedname=taxon->name;
classname="scientific name";
if (name)
{
classname=name->classname;
matchedname=name->name;
}
rankname= taxonomy->ranks->label[taxon->rank]; rankname= taxonomy->ranks->label[taxon->rank];
printf("%10d \t| %15s \t|\t %s\n", printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s\n",
taxon->taxid, taxon->taxid,
rankname, rankname,
matchedname,
classname,
taxon->name); taxon->name);
} }
/**
* display header before printing any result
**/
static void printheader(void)
{
printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s\n#\n",
"taxonomy id",
"taxonomy rank",
"name",
"class name",
"scientific name");
}
/**
* display son's list for given taxon
**/
static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count)
{
int32_t i;
ecotx_t *current_taxon;
for ( i = 0, current_taxon = taxonomy->taxons->taxon;
i < taxonomy->taxons->count;
i++, current_taxon++)
{
if (taxon->taxid == current_taxon->parent->taxid)
{
(*count)++;
printresult(current_taxon, NULL, taxonomy);
get_son(taxonomy,current_taxon,count);
}
}
}
/**
* display list of rank filter option (-l option)
**/
static void listfilteroptions(ecorankidx_t *ranks)
{
int32_t i;
printf("#\n");
for ( i=0;
i < ranks->count;
i++)
{
printf("# %s \n",ranks->label[i]);
}
printf("#\n");
}
/* ---------------------------------------- */ /* ---------------------------------------- */
/* get back on given taxid taxonomic parent */ /* get back on given taxid taxonomic parent */
@ -33,16 +100,16 @@ void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy)
next_parent = eco_findtaxonbytaxid(taxonomy, taxid); next_parent = eco_findtaxonbytaxid(taxonomy, taxid);
printf("# taxonomy id \t|\t taxonomy rank \t|\t scientific name\n#\n"); printheader();
while ( strcmp(next_parent->name, "root") ) while ( strcmp(next_parent->name, "root") )
{ {
printresult(next_parent, taxonomy); printresult(next_parent, NULL,taxonomy);
next_parent = next_parent->parent; next_parent = next_parent->parent;
c++; c++;
} }
printf("# %d parents found\n#\n",c); printf("# %d parent(s) found\n#\n",c);
} }
@ -54,7 +121,7 @@ void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy)
static void ExitUsage(stat) static void ExitUsage(stat)
int stat; int stat;
{ {
PP "usage: ecofind [-d database] [-h] [-t taxid] <taxon name pattern> ... \n"); PP "usage: ecofind [-d database] [-h] [-l] [-r taxonomic rank] [-p taxid] [-s taxid] <taxon name pattern> ... \n");
PP "type \"ecofind -h\" for help\n"); PP "type \"ecofind -h\" for help\n");
if (stat) if (stat)
exit(stat); exit(stat);
@ -84,8 +151,12 @@ static void PrintHelp()
PP " program located in the tools directory.\n"); PP " program located in the tools directory.\n");
PP " Write the database radical without any extension.\n\n"); PP " Write the database radical without any extension.\n\n");
PP "-h : [H]elp - print <this> help\n\n"); PP "-h : [H]elp - print <this> help\n\n");
PP "-t : [T]axonomic id. Specifiying this option will display"); PP "-l : [L]ist all taxonomic rank available for -r option\n\n");
PP " all parents parent information for the given taxid."); PP "-p : [P]arent's taxonomic id. Specifiying this option will display ");
PP " all parent's information for the given taxid.\n\n");
PP "-r : [R]estrict to given taxonomic rank\n\n");
PP "-s : [S]on's taxonomic id. Specifiying this option will display ");
PP " all son's information for the given taxid.\n\n");
PP "<taxon> name pattern bearing regular expressions\n\n"); PP "<taxon> name pattern bearing regular expressions\n\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n"); PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n");
@ -105,20 +176,49 @@ int main(int argc, char **argv)
int32_t k,j = 0; int32_t k,j = 0;
int32_t errflag = 0; int32_t errflag = 0;
int32_t tax_count = 0; int32_t tax_count = 0;
int32_t alternative = 0;
char *prefix = NULL; char *prefix = NULL;
ecotx_t *taxon = NULL;
ecotaxonomy_t *taxonomy; ecotaxonomy_t *taxonomy;
econame_t *name;
int32_t name_count;
int re_error; int re_error;
int re_match; int re_match;
regex_t re_preg; regex_t re_preg;
int32_t taxid = 0; int32_t uptree = 0;
int32_t subtree = 0;
char *rankname = NULL;
int32_t rankfilter = 1;
int32_t list = 0;
while ((carg = getopt(argc, argv, "hd:t:")) != -1) { ecotx_t *subtree_parent;
int32_t count_son = 0;
while ((carg = getopt(argc, argv, "had:p:s:r:l")) != -1) {
switch (carg) { switch (carg) {
case 's': /* path to the database */
sscanf(optarg,"%d",&subtree);
break;
case 'r': /* rank filter */
rankname = ECOMALLOC(strlen(optarg),"allocation rankname");
strcpy(rankname,optarg);
rankfilter = 0;
break;
case 'd': /* path to the database */ case 'd': /* path to the database */
prefix = optarg; prefix = ECOMALLOC(strlen(optarg),"allocation prefix");
strcpy(prefix,optarg);
break;
case 'l': /* list rank filter options */
list = 1;
break;
case 'a': /* allow alternative names */
alternative = 1;
break; break;
case 'h': /* display help */ case 'h': /* display help */
@ -126,8 +226,8 @@ int main(int argc, char **argv)
exit(0); exit(0);
break; break;
case 't': /* taxid */ case 'p': /* taxid */
sscanf(optarg,"%d",&taxid); sscanf(optarg,"%d",&uptree);
break; break;
case '?': /* bad option */ case '?': /* bad option */
@ -145,7 +245,7 @@ int main(int argc, char **argv)
errflag++; errflag++;
} }
if (errflag && !taxid) if (errflag && !uptree && !rankname && !subtree)
ExitUsage(errflag); ExitUsage(errflag);
/** /**
@ -153,21 +253,46 @@ int main(int argc, char **argv)
**/ **/
printf("# \n# opening %s database\n",prefix); printf("# \n# opening %s database\n",prefix);
taxonomy = read_taxonomy(prefix); taxonomy = read_taxonomy(prefix,1);
tax_count = taxonomy->taxons->count; tax_count = taxonomy->taxons->count;
name_count = taxonomy->names->count;
printf("# %d taxons\n", tax_count);
/* ---------------------------------------- */
/* list -r option possibility */
/* ---------------------------------------- */
if (list)
{
listfilteroptions(taxonomy->ranks);
return 0;
}
/* ---------------------------------------- */ /* ---------------------------------------- */
/* display taxid parent if -t option */ /* display taxid parent if -t option */
/* specified in command line */ /* specified in command line */
/* ---------------------------------------- */ /* ---------------------------------------- */
if (taxid) if (uptree)
{ {
gettaxidparents(taxid,taxonomy); gettaxidparents(uptree,taxonomy);
return 0; return 0;
} }
/* ---------------------------------------- */
/* display taxid sons if -s option */
/* specified in command line */
/* ---------------------------------------- */
if (subtree)
{
printheader();
subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
get_son(taxonomy, subtree_parent,&count_son);
printf("# %d son(s) found\n#\n",count_son);
return 0;
}
printf("# %d taxons\n", tax_count);
/** /**
* parse taxonomy * parse taxonomy
**/ **/
@ -184,18 +309,24 @@ int main(int argc, char **argv)
nummatch=0; nummatch=0;
printf("# taxonomy id \t|\t taxonomy rank \t|\t scientific name\n#\n"); printheader();
for (j=0,taxon=taxonomy->taxons->taxon; for (j=0,name=taxonomy->names->names;
j < tax_count; j < name_count;
taxon++,j++) name++,j++)
{ {
re_match = regexec (&re_preg, taxon->name, 0, NULL, 0);
if (re_match == 0) if(rankname)
rankfilter = !(strcmp(rankname,taxonomy->ranks->label[name->taxon->rank]));
re_match = regexec (&re_preg, name->name, 0, NULL, 0);
if (!re_match && (alternative || name->is_scientificname) && rankfilter)
{ {
printresult(taxon,taxonomy); printresult(name->taxon,name,taxonomy);
nummatch++; nummatch++;
} }
} }
printf("# %d records found \n",nummatch); printf("# %d records found \n",nummatch);