obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Taxonomy: functions to read the *.adx file (containing the deprecated

Browse Source 
and current taxids and their corresponding indices in the taxa
structure) and to find the taxa using the merged index.
This commit is contained in:
Celine Mercier
2017-01-06 15:52:21 +01:00
parent f396625f98
commit d68374018b
2 changed files with 132 additions and 9 deletions
Download Patch File Download Diff File Expand all files Collapse all files

140
src/obidms_taxonomy.c
View File

@ -35,7 +35,7 @@ int cmp_rank_labels(const void* label1, const void* label2)
}
static int cmp_taxids(const void* ptaxid, const void* ptaxon)
static int cmp_taxids_in_ecotx_t(const void* ptaxid, const void* ptaxon)
{
ecotx_t* current_taxon = (ecotx_t*) ptaxon;
int32_t taxid = (int32_t) ((size_t) ptaxid);
@ -43,6 +43,14 @@ static int cmp_taxids(const void* ptaxid, const void* ptaxon)
}
static int cmp_taxids_in_ecomerged_t(const void* ptaxid, const void* ptaxon)
{
ecomerged_t* current_taxon = (ecomerged_t*) ptaxon;
int32_t taxid = (int32_t) ((size_t) ptaxid);
return taxid - current_taxon->taxid;
}
static int cmp_str(const void* s1, const void* s2)
{
return strcmp(*((char**)s1), *((char**)s2));
@ -467,6 +475,55 @@ econameidx_t* read_nameidx(const char *file_name, OBIDMS_taxonomy_p taxonomy)
ecomergedidx_t* read_mergedidx(const char *file_name, OBIDMS_taxonomy_p taxonomy)
{
int32_t count;
FILE* f;
ecomergedidx_t* index_merged_idx;
ecomerged_t* merged_idx;
int32_t i;
int32_t record_length;
f = open_ecorecorddb(file_name, &count, 0);
if (f == NULL)
{
obidebug(1, "\nError reading taxonomy name file");
return NULL;
}
index_merged_idx = (ecomergedidx_t*) malloc(sizeof(ecomergedidx_t) + (sizeof(ecomerged_t) * count));
if (index_merged_idx == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError reading taxonomy name file");
return NULL;
}
index_merged_idx->count = count;
for (i=0; i < count; i++)
{
merged_idx = read_ecorecord(f, &record_length);
memcpy((index_merged_idx->merged)+i, merged_idx, record_length);
if ((index_merged_idx->merged)+i == NULL)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError reading taxonomy name file");
free(index_merged_idx);
return NULL;
}
}
fclose(f);
return index_merged_idx;
}
// Functions to write taxonomy structure to binary files
@ -1003,6 +1060,7 @@ int write_mergedidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_na
int file_descriptor;
off_t file_size;
char* taxonomy_path;
int32_t record_size;
// Compute file size
file_size = sizeof(int32_t) + (sizeof(int32_t) * 3 * (tax->merged_idx)->count);
@ -1058,9 +1116,20 @@ int write_mergedidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_na
return -1;
}
record_size = 2 * sizeof(int32_t);
// Write merged indices
for (i=0; i < (tax->merged_idx)->count; i++)
{
// Write record size
if (write(file_descriptor, &(record_size), sizeof(int32_t)) < ((ssize_t) sizeof(int32_t)))
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError writing in a binary taxonomy file");
close(file_descriptor);
return -1;
}
// Write taxid
if (write(file_descriptor, &(((tax->merged_idx)->merged)[i].taxid), sizeof(int32_t)) < ((ssize_t) sizeof(int32_t)))
{
@ -1566,7 +1635,7 @@ OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump)
// Store the deprecated taxid with the index that refers to the new taxid
// Find the index of the new taxid
t = obi_taxo_get_taxon_with_taxid(tax, taxid);
t = obi_taxo_get_taxon_with_current_taxid(tax, taxid);
// Store the old taxid with the index
(tax->merged_idx)->merged[n].taxid = old_taxid;
(tax->merged_idx)->merged[n].idx = t->idx;
@ -1966,7 +2035,7 @@ OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump)
// Associate the taxa with their parent
for (i=0; i < (tax->taxa)->count; i++)
{
((tax->taxa)->taxon)[i].parent = obi_taxo_get_taxon_with_taxid(tax, parent_taxids[i]);
((tax->taxa)->taxon)[i].parent = obi_taxo_get_taxon_with_current_taxid(tax, parent_taxids[i]);
if (((tax->taxa)->taxon)[i].parent == NULL)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
@ -2129,6 +2198,7 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
char* taxonomy_path;
char* ranks_file_name;
char* taxa_file_name;
char* merged_idx_file_name;
char* local_taxa_file_name;
char* alter_names_file_name;
int buffer_size;
@ -2238,6 +2308,35 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
free(taxa_file_name);
free(local_taxa_file_name);
// Read merged index (old and current taxids referring to indices in the taxa structure)
merged_idx_file_name = (char*) malloc(buffer_size*sizeof(char));
if (merged_idx_file_name == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for merged index file name");
free(taxonomy_path);
obi_close_taxonomy(tax);
return NULL;
}
if (snprintf(merged_idx_file_name, buffer_size, "%s/%s.adx", taxonomy_path, taxonomy_name) < 0)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError building merged index file name");
free(taxonomy_path);
free(merged_idx_file_name);
obi_close_taxonomy(tax);
return NULL;
}
tax->merged_idx = read_mergedidx(merged_idx_file_name, tax);
if (tax->merged_idx == NULL)
{
free(taxonomy_path);
free(merged_idx_file_name);
obi_close_taxonomy(tax);
return NULL;
}
free(merged_idx_file_name);
// Read alternative names
if (read_alternative_names)
{
@ -2363,10 +2462,10 @@ ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
}
ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
ecotx_t* obi_taxo_get_taxon_with_current_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid) // TODO discuss keeping private?
{
ecotx_t *current_taxon;
int32_t count;
ecotx_t *current_taxon;
int32_t count;
count = (taxonomy->taxa)->count;
@ -2374,12 +2473,35 @@ ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid
(const void *) taxonomy->taxa->taxon,
count,
sizeof(ecotx_t),
cmp_taxids);
cmp_taxids_in_ecotx_t);
return current_taxon;
}
bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
{
ecotx_t *current_taxon;
ecomerged_t *indexed_taxon;
int32_t count;
count = (taxonomy->merged_idx)->count;
indexed_taxon = (ecomerged_t*) bsearch((const void *) ((size_t) taxid),
(const void *) taxonomy->merged_idx->merged,
count,
sizeof(ecomerged_t),
cmp_taxids_in_ecomerged_t);
if (indexed_taxon == NULL)
current_taxon = NULL;
else
current_taxon = (taxonomy->taxa->taxon)+(indexed_taxon->idx);
return current_taxon;
}
bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid) // TODO discuss that this doesn't work with deprecated taxids
{
ecotx_t* next_parent;
@ -2486,7 +2608,7 @@ ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
{
static OBIDMS_taxonomy_p tax = NULL;
static int32_t rankindex = -1;
static int32_t rankindex = -1;
if (taxonomy && (tax != taxonomy))
{

1
src/obidms_taxonomy.h
View File

@ -108,6 +108,7 @@ int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
ecotx_t* obi_taxo_get_taxon_with_current_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);