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version 0.5: ecoPrimers can now read *.ldx files (local taxa)

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This commit is contained in:
Celine Mercier
2019-01-22 15:51:43 +01:00
parent eb8d44528d
commit 73236c72a8
4 changed files with 34 additions and 13 deletions
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2
VERSION
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@ -1 +1 @@
0.4 0.5

2
src/ecoprimer.c
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@ -20,7 +20,7 @@
#include"libthermo/thermostats.h" #include"libthermo/thermostats.h"
#define VERSION "0.4" #define VERSION "0.5"
/* TR: by default, statistics are made on species level*/ /* TR: by default, statistics are made on species level*/
#define DEFAULTTAXONRANK "species" #define DEFAULTTAXONRANK "species"

2
src/libecoPCR/ecoPCR.h
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@ -219,7 +219,7 @@ 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);

41
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,"Reading %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 + (size_t)index->taxon[i].parent; index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
} }
if (count2>0)
fprintf(stderr,"Reading %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;
} }
@ -111,33 +129,36 @@ 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),
"Allocate taxonomy structure"); "Allocate taxonomy structure");
buffsize = strlen(prefix)+10; buffsize = strlen(prefix)+10;
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)
{ {
snprintf(filename,buffsize,"%s.ndx",prefix); snprintf(filename,buffsize,"%s.ndx",prefix);
tax->names=read_nameidx(filename,tax); tax->names=read_nameidx(filename,tax);
} }
else else
tax->names=NULL; tax->names=NULL;
return tax; return tax;
} }