Merge pull request #142 from dfornika/names-to-taxids-141

Add missing args to initETE3Database
phac-nml · Jun 30, 2023 · af3014b · af3014b
2 parents 5126ee7 + 5a5e8af
commit af3014b
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Showing 3 changed files with 17 additions and 17 deletions.
diff --git a/mob_suite/mob_cluster.py b/mob_suite/mob_cluster.py
@@ -533,7 +533,7 @@ def main():
             new_seq_info[seq_id]['organism'] = organism
 
     ETE3DBTAXAFILE = os.path.abspath(database_dir + "/taxa.sqlite")
-    taxids = NamesToTaxIDs(organisms, ETE3DBTAXAFILE)
+    taxids = NamesToTaxIDs(organisms, ETE3DBTAXAFILE, database_dir)
     del(organisms)
 
     for seq_id in new_seq_info:

diff --git a/mob_suite/mob_typer.py b/mob_suite/mob_typer.py
@@ -508,7 +508,7 @@ def main():
             record['relaxase_type_accession(s)'] = ",".join(record['relaxase_type_accession(s)'])
 
         host_range = hostrange(record['rep_type(s)'].split(','), record['relaxase_type_accession(s)'].split(','),
-                               mob_cluster_id, ncbi, lit,ETE3DBTAXAFILE)
+                               mob_cluster_id, ncbi, lit, ETE3DBTAXAFILE, database_dir)
 
         for field in host_range:
             record[field] = host_range[field]

diff --git a/mob_suite/utils.py b/mob_suite/utils.py
@@ -79,10 +79,10 @@ def filter_invalid_taxids(taxids):
     return filtered
 
 
-def getHeirarchy(taxid,ETE3DBTAXAFILE):
+def getHeirarchy(taxid,ETE3DBTAXAFILE,database_directory):
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
         logging.info("Did not find taxa.sqlite in {}. Initializaing ete3 taxonomy database".format(ETE3DBTAXAFILE))
-        initETE3Database()
+        initETE3Database(database_directory, ETE3DBTAXAFILE)
 
     ncbi = NCBITaxa(dbfile=ETE3DBTAXAFILE)
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
@@ -103,10 +103,10 @@ def getHeirarchy(taxid,ETE3DBTAXAFILE):
     return {'names': names, 'ranks': names}
 
 
-def getTaxid(taxon,ETE3DBTAXAFILE):
+def getTaxid(taxon,ETE3DBTAXAFILE,database_directory):
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
         logging.info("Did not find taxa.sqlite in {}. Initializaing ete3 taxonomy database".format(ETE3DBTAXAFILE))
-        initETE3Database()
+        initETE3Database(database_directory, ETE3DBTAXAFILE)
 
     ncbi = NCBITaxa(dbfile=ETE3DBTAXAFILE)
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
@@ -121,10 +121,10 @@ def getTaxid(taxon,ETE3DBTAXAFILE):
 
 
 
-def NamesToTaxIDs(names,ETE3DBTAXAFILE):
+def NamesToTaxIDs(names,ETE3DBTAXAFILE,database_directory):
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
         logging.info("Did not find taxa.sqlite in {}. Initializaing ete3 taxonomy database".format(ETE3DBTAXAFILE))
-        initETE3Database(ETE3DBTAXAFILE)
+        initETE3Database(database_directory, ETE3DBTAXAFILE)
 
     ncbi = NCBITaxa(dbfile=ETE3DBTAXAFILE)
 
@@ -138,10 +138,10 @@ def NamesToTaxIDs(names,ETE3DBTAXAFILE):
 
 
 
-def getTaxonConvergence(taxids,ETE3DBTAXAFILE):
+def getTaxonConvergence(taxids,ETE3DBTAXAFILE,database_directory):
     if not isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
         logging.info("Did not find taxa.sqlite in {}. Initializaing ete3 taxonomy database".format(ETE3DBTAXAFILE))
-        initETE3Database(ETE3DBTAXAFILE)
+        initETE3Database(database_directory, ETE3DBTAXAFILE)
 
     ncbi = NCBITaxa(dbfile=ETE3DBTAXAFILE)
 
@@ -206,7 +206,7 @@ def getTaxonConvergence(taxids,ETE3DBTAXAFILE):
     return (['-', '-'])
 
 
-def hostrange(replion_types, relaxase_types, mob_cluster_id, ncbi, lit,ETE3DBTAXAFILE):
+def hostrange(replion_types, relaxase_types, mob_cluster_id, ncbi, lit, ETE3DBTAXAFILE, database_directory):
     host_range_predictions = {
         'observed_host_range_ncbi_name': '',
         'observed_host_range_ncbi_rank': '',
@@ -251,25 +251,25 @@ def hostrange(replion_types, relaxase_types, mob_cluster_id, ncbi, lit,ETE3DBTAX
         ncbi_unique_taxids = filter_invalid_taxids(
             list(set(ncbi_replicon_taxids + ncbi_cluster_taxids + ncbi_relaxase_taxids)))
         host_range_predictions['observed_host_range_ncbi_rank'], host_range_predictions[
-            'observed_host_range_ncbi_name'] = getTaxonConvergence(ncbi_unique_taxids,ETE3DBTAXAFILE)
+            'observed_host_range_ncbi_name'] = getTaxonConvergence(ncbi_unique_taxids,ETE3DBTAXAFILE,database_directory)
 
     # Determine taxids associated with literature
 
     lit_unique_taxids = filter_invalid_taxids(list(set(lit_replicon_taxids)))
 
     host_range_predictions['reported_host_range_lit_rank'], host_range_predictions[
-        'reported_host_range_lit_name'] = getTaxonConvergence(lit_unique_taxids,ETE3DBTAXAFILE)
+        'reported_host_range_lit_name'] = getTaxonConvergence(lit_unique_taxids,ETE3DBTAXAFILE,database_directory)
 
     # determine overall host range
     overall_taxids = filter_invalid_taxids(list(set(ncbi_unique_taxids + lit_unique_taxids)))
     host_range_predictions['predicted_host_range_overall_rank'], host_range_predictions[
-        'predicted_host_range_overall_name'] = getTaxonConvergence(overall_taxids,ETE3DBTAXAFILE)
+        'predicted_host_range_overall_name'] = getTaxonConvergence(overall_taxids,ETE3DBTAXAFILE,database_directory)
 
     # move host-range prediction up to family when it is at genus or species level
     if host_range_predictions['predicted_host_range_overall_rank'] == 'genus' or host_range_predictions[
         'predicted_host_range_overall_rank'] == 'species':
-        taxid = getTaxid(host_range_predictions['predicted_host_range_overall_name'],ETE3DBTAXAFILE)
-        heir = getHeirarchy(taxid,ETE3DBTAXAFILE)
+        taxid = getTaxid(host_range_predictions['predicted_host_range_overall_name'],ETE3DBTAXAFILE,database_directory)
+        heir = getHeirarchy(taxid,ETE3DBTAXAFILE,database_directory)
         names = heir['names']
         ranks = heir['ranks']
 
@@ -369,7 +369,7 @@ def isETE3DBTAXAFILEexists(ETE3DBTAXAFILE):
         return True
 
 
-def initETE3Database(database_directory, ETE3DBTAXAFILE, logging):
+def initETE3Database(database_directory, ETE3DBTAXAFILE):
     lockfilepath = os.path.join(database_directory, ".lock")
 
     if os.path.exists(lockfilepath) == False: