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Add management of local taxa from the new extension of the OBI Taxonomy library

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@315 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2011-07-19 06:44:47 +00:00
parent 9adf426abf
commit 957a59eb5d
4 changed files with 31 additions and 8 deletions
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1
src/ecopcr.c
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@ -527,6 +527,7 @@ int main(int argc, char **argv)
o1c = complementPattern(o1); o1c = complementPattern(o1);
o2c = complementPattern(o2); o2c = complementPattern(o2);
printf("#@ecopcr-v2\n");
printf("#\n"); printf("#\n");
printf("# ecoPCR version %s\n",VERSION); printf("# ecoPCR version %s\n",VERSION);
printf("# direct strand oligo1 : %-32s ; oligo2c : %32s\n", o1->cpat,o2c->cpat); printf("# direct strand oligo1 : %-32s ; oligo2c : %32s\n", o1->cpat,o2c->cpat);

2
src/libecoPCR/ecoPCR.h
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@ -220,7 +220,7 @@ econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
* @return pointer to a taxonomy index structure * @return pointer to a taxonomy index structure
*/ */
ecotxidx_t *read_taxonomyidx(const char *filename); ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2);
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName); ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);

2
src/libecoPCR/ecoseq.c
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@ -169,7 +169,7 @@ FILE *open_seqfile(const char *prefix,int32_t index)
prefix, prefix,
index); index);
fprintf(stderr,"# Coucou %s\n",filename_buffer); // fprintf(stderr,"# Coucou %s\n",filename_buffer);
if (filename_length >= 1024) if (filename_length >= 1024)

34
src/libecoPCR/ecotax.c
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@ -10,23 +10,41 @@ static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
* @param pointer to the database (.tdx file) * @param pointer to the database (.tdx file)
* @return a ecotxidx_t structure * @return a ecotxidx_t structure
*/ */
ecotxidx_t *read_taxonomyidx(const char *filename) ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2)
{ {
int32_t count; int32_t count;
int32_t count2;
FILE *f; FILE *f;
FILE *f2;
ecotxidx_t *index; ecotxidx_t *index;
int32_t i; int32_t i;
f = open_ecorecorddb(filename,&count,1); f = open_ecorecorddb(filename,&count,1);
f2 = open_ecorecorddb(filename2,&count2,0);
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1), index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
"Allocate taxonomy"); "Allocate taxonomy");
index->count=count; index->count=count+count2;
fprintf(stderr,"Readind %d taxa...\n",count);
for (i=0; i < count; i++){ for (i=0; i < count; i++){
readnext_ecotaxon(f,&(index->taxon[i])); readnext_ecotaxon(f,&(index->taxon[i]));
index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent; index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
} }
if (count2>0)
fprintf(stderr,"Readind %d local taxa...\n",count2);
else
fprintf(stderr,"No local taxon\n");
for (i=0; i < count2; i++){
readnext_ecotaxon(f2,&(index->taxon[count+i]));
index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
}
return index; return index;
} }
@ -111,6 +129,7 @@ ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName)
{ {
ecotaxonomy_t *tax; ecotaxonomy_t *tax;
char *filename; char *filename;
char *filename2;
int buffsize; int buffsize;
tax = ECOMALLOC(sizeof(ecotaxonomy_t), tax = ECOMALLOC(sizeof(ecotaxonomy_t),
@ -120,14 +139,17 @@ ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName)
filename = ECOMALLOC(buffsize, filename = ECOMALLOC(buffsize,
"Allocate filename"); "Allocate filename");
filename2= ECOMALLOC(buffsize,
"Allocate filename");
snprintf(filename,buffsize,"%s.rdx",prefix); snprintf(filename,buffsize,"%s.rdx",prefix);
tax->ranks = read_rankidx(filename); tax->ranks = read_rankidx(filename);
snprintf(filename,buffsize,"%s.tdx",prefix); snprintf(filename,buffsize,"%s.tdx",prefix);
snprintf(filename2,buffsize,"%s.ldx",prefix);
tax->taxons = read_taxonomyidx(filename); tax->taxons = read_taxonomyidx(filename,filename2);
if (readAlternativeName) if (readAlternativeName)
{ {
@ -326,4 +348,4 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined"); ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
return eco_findtaxonatrank(taxon,rankindex); return eco_findtaxonatrank(taxon,rankindex);
} }