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

ecotag: trying to use a threshold lower than the ref db threshold now

Browse Source 
returns an error instead of a warning
This commit is contained in:
Celine Mercier
2019-09-15 19:27:47 +02:00
parent f8d1fa678a
commit eb913b2742
2 changed files with 9 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
python/obitools3/commands/ecotag.pyx
View File

@ -63,6 +63,11 @@ def run(config):
ref_dms_name = ref[0].name ref_dms_name = ref[0].name
ref_view_name = ref[1] ref_view_name = ref[1]
# Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
if config['ecotag']['threshold'] < eval(i_dms[ref_view_name].comments["ref_db_threshold"]) :
print("Error: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).",
config['ecotag']['threshold'], i_dms[ref_view_name].comments["ref_db_threshold"])
# Open the output: only the DMS # Open the output: only the DMS
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
input=False, input=False,

7
src/obi_ecotag.c
View File

@ -365,10 +365,11 @@ int obi_ecotag(const char* dms_name,
} }
free(db_threshold_str); free(db_threshold_str);
if (ecotag_threshold < db_threshold) if (ecotag_threshold < db_threshold)
fprintf(stderr, "\nWarning: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f). " {
"\n\tMeaning that the similarity *between reference sequences* below the ref db threshold will not be considered. " fprintf(stderr, "\nError: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).\n\n",
"\n\tEcotag normally uses that similarity for better results but it works fine without it.\n\n",
ecotag_threshold, db_threshold); ecotag_threshold, db_threshold);
return -1;
}
// Open the ID column of reference sequences // Open the ID column of reference sequences
ref_id_column = obi_view_get_column(ref_view, ID_COLUMN); ref_id_column = obi_view_get_column(ref_view, ID_COLUMN);