From 1b346b54f9630a6bb1829d3c791da92657c300e2 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Tue, 28 Apr 2020 15:10:07 +0200 Subject: [PATCH] ecotag: better specificity by now correctly looking for similarities within refs above best score instead of ecotag threshold --- python/obitools3/version.py | 2 +- src/obi_ecotag.c | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/python/obitools3/version.py b/python/obitools3/version.py index 65834bb..d8a4269 100755 --- a/python/obitools3/version.py +++ b/python/obitools3/version.py @@ -1,5 +1,5 @@ major = 3 minor = 0 -serial= '0-beta14d' +serial= '0-beta14e' version ="%d.%02d.%s" % (major,minor,serial) diff --git a/src/obi_ecotag.c b/src/obi_ecotag.c index b498cfa..dcd6dac 100755 --- a/src/obi_ecotag.c +++ b/src/obi_ecotag.c @@ -455,7 +455,7 @@ int obi_ecotag(const char* dms_name, for (i=0; i < query_count; i++) { - if (i%100 == 0) + if (i%1000 == 0) fprintf(stderr,"\rDone : %f %% ", (i / (float) query_count)*100); 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); k = 0; - while ((k < lca_array_length) && (score_array[k] >= ecotag_threshold)) + while ((k < lca_array_length) && (score_array[k] >= best_score)) k++; 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); if (j>0) { - lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid); - if (lca == NULL) - { - obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment"); - return -1; - } +// lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid); +// if (lca == NULL) +// { +// obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment"); +// return -1; +// } lca_in_array = obi_taxo_get_taxon_with_taxid(taxonomy, lca_array[k-1]); if (lca_in_array == NULL) {