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ecotag: better specificity by now correctly looking for similarities

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within refs above best score instead of ecotag threshold
This commit is contained in:
Celine Mercier
2020-04-28 15:10:07 +02:00
parent 058f2ad8b3
commit 1b346b54f9
2 changed files with 9 additions and 9 deletions
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2
python/obitools3/version.py
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@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '0-beta14d' serial= '0-beta14e'
version ="%d.%02d.%s" % (major,minor,serial) version ="%d.%02d.%s" % (major,minor,serial)

16
src/obi_ecotag.c
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@ -455,7 +455,7 @@ int obi_ecotag(const char* dms_name,
for (i=0; i < query_count; i++) for (i=0; i < query_count; i++)
{ {
if (i%100 == 0) if (i%1000 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) query_count)*100); fprintf(stderr,"\rDone : %f %% ", (i / (float) query_count)*100);
best_match_count = 0; best_match_count = 0;
@ -562,7 +562,7 @@ int obi_ecotag(const char* dms_name,
score_array = obi_get_array_with_col_p_in_view(ref_view, score_a_column, best_match_idx, &lca_array_length); score_array = obi_get_array_with_col_p_in_view(ref_view, score_a_column, best_match_idx, &lca_array_length);
k = 0; k = 0;
while ((k < lca_array_length) && (score_array[k] >= ecotag_threshold)) while ((k < lca_array_length) && (score_array[k] >= best_score))
k++; k++;
if (k>0) if (k>0)
@ -570,12 +570,12 @@ int obi_ecotag(const char* dms_name,
lca_array = obi_get_array_with_col_p_in_view(ref_view, lca_taxid_a_column, best_match_idx, &lca_array_length); lca_array = obi_get_array_with_col_p_in_view(ref_view, lca_taxid_a_column, best_match_idx, &lca_array_length);
if (j>0) if (j>0)
{ {
lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid); // lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid);
if (lca == NULL) // if (lca == NULL)
{ // {
obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment"); // obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment");
return -1; // return -1;
} // }
lca_in_array = obi_taxo_get_taxon_with_taxid(taxonomy, lca_array[k-1]); lca_in_array = obi_taxo_get_taxon_with_taxid(taxonomy, lca_array[k-1]);
if (lca_in_array == NULL) if (lca_in_array == NULL)
{ {