obitools/ecoprimers
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 2 Wiki Activity

with full coverage statistic

Browse Source 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@187 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-15 21:52:06 +00:00
parent 665b22989f
commit 9908a40aaa
1 changed files with 95 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files

113
src/libecoprimer/taxstats.c
View File

@ -6,41 +6,118 @@
*/ */
#include <search.h> #include <search.h>
#include "ecoprimer.h"
static int cmptaxon(void *t1, void* t2); static int cmptaxon(const void *t1, const void* t2);
static int cmptaxon(const void *t1, const void* t2)
static int cmptaxon(void *t1, void* t2)
{ {
if (*t1 < *t2) const size_t taxid1=(size_t)t1;
const size_t taxid2=(size_t)t2;
// fprintf(stderr,"==> counted taxid1 : %d\n",taxid1);
// fprintf(stderr,"==> counted taxid2 : %d\n",taxid2);
if (taxid1 < taxid2)
return -1; return -1;
if (*t1 > *t2) if (taxid1 > taxid2)
return +1; return +1;
return 0; return 0;
} }
int32_t counttaxon(int32_t taxid)
{
static void* taxontree=NULL;
static int32_t taxoncount=0;
// fprintf(stderr,"counted taxid : %d taxontree %p\n",taxid,taxontree);
if (taxid==-1)
{
if (taxontree)
ECOFREE(taxontree,"Free taxon tree");
taxontree=NULL;
taxoncount=0;
return 0;
}
if ((!taxontree) || (!tfind((void*)((size_t)taxid),&taxontree,cmptaxon)))
{
tsearch((void*)((size_t)taxid),&taxontree,cmptaxon);
taxoncount++;
}
return taxoncount;
}
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options)
{
uint32_t i;
uint32_t j;
ecotx_t *taxon;
ecotx_t *tmptaxon;
counttaxon(-1);
for (i=0;i<seqdbsize;i++)
{
taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
tmptaxon = eco_findtaxonatrank(taxon,
options->taxonrankidx);
// fprintf(stderr,"Taxid : %d %p\n",taxon->taxid,tmptaxon);
if (tmptaxon)
{
// fprintf(stderr,"orig : %d trans : %d\n",taxon->taxid,
// tmptaxon->taxid);
seqdb[i]->ranktaxonid=tmptaxon->taxid;
if (seqdb[i]->isexample)
options->intaxa = counttaxon(tmptaxon->taxid);
}
else
seqdb[i]->ranktaxonid=-1;
}
counttaxon(-1);
for (i=0;i<seqdbsize;i++)
{
if (seqdb[i]->ranktaxonid>=0 && !seqdb[i]->isexample)
options->outtaxa = counttaxon(seqdb[i]->ranktaxonid);
}
return options->outtaxa + options->intaxa;
}
float taxonomycoverage(ppair_t pair, poptions_t options) float taxonomycoverage(ppair_t pair, poptions_t options)
{ {
int32_t seqcount; int32_t seqcount;
int32_t *taxon;
int32_t i; int32_t i;
void **taxontree; int32_t incount=0;
ppair_t *inserted; int32_t outcount=0;
int32_t taxoncount;
seqcount=pair->pcr.ampcount; seqcount=pair->pcr.ampcount;
taxon = ECOMALLOC(seqcount * sizeof(int32_t));
taxoncount=0;
taxontree=NULL;
counttaxon(-1);
for (i=0; i < seqcount; i++) for (i=0; i < seqcount; i++)
if (pair->pcr.amplifias[i].sequence->isexample) if (pair->pcr.amplifias[i].sequence->isexample)
{ incount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
inserted = tsearch(pair->pcr.amplifias[i].sequence->ranktaxonid,
taxontree,
cmptaxon);
}
counttaxon(-1);
for (i=0; i < seqcount; i++)
if (!pair->pcr.amplifias[i].sequence->isexample)
outcount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
pair->intaxa=incount;
pair->outtaxa=outcount;
return (float)incount/options->intaxa;
} }