Merge pull request #149 from rpetit3/master

fix hostrange() missing 1 required positional argument: 'database_directory'
phac-nml · Aug 14, 2023 · 7d758d1 · 7d758d1
2 parents 2231520 + 3067a12
commit 7d758d1
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Showing 3 changed files with 13 additions and 14 deletions.
diff --git a/mob_suite/mob_recon.py b/mob_suite/mob_recon.py
@@ -1392,7 +1392,7 @@ def main():
             mobtyper_report = os.path.join(out_dir, "mobtyper_results.txt")
             if prefix is not None:
                 mobtyper_report = os.path.join(out_dir, "{}.mobtyper_results.txt".format(prefix))
-            build_mobtyper_report(contig_memberships['plasmid'], out_dir, mobtyper_report,contig_seqs, ncbi, lit,ETE3DBTAXAFILE)
+            build_mobtyper_report(contig_memberships['plasmid'], out_dir, mobtyper_report,contig_seqs, ncbi, lit, ETE3DBTAXAFILE, database_dir)
 
         writeReport(results, MOB_RECON_INFO_HEADER, contig_report)
 

diff --git a/mob_suite/utils.py b/mob_suite/utils.py
@@ -79,7 +79,7 @@ def filter_invalid_taxids(taxids):
     return filtered
 
 
-def getHeirarchy(taxid,ETE3DBTAXAFILE,database_directory):
+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(database_directory, ETE3DBTAXAFILE)
@@ -103,7 +103,7 @@ def getHeirarchy(taxid,ETE3DBTAXAFILE,database_directory):
     return {'names': names, 'ranks': names}
 
 
-def getTaxid(taxon,ETE3DBTAXAFILE,database_directory):
+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(database_directory, ETE3DBTAXAFILE)
@@ -121,7 +121,7 @@ def getTaxid(taxon,ETE3DBTAXAFILE,database_directory):
 
 
 
-def NamesToTaxIDs(names,ETE3DBTAXAFILE,database_directory):
+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(database_directory, ETE3DBTAXAFILE)
@@ -138,7 +138,7 @@ def NamesToTaxIDs(names,ETE3DBTAXAFILE,database_directory):
 
 
 
-def getTaxonConvergence(taxids,ETE3DBTAXAFILE,database_directory):
+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(database_directory, ETE3DBTAXAFILE)
@@ -251,25 +251,25 @@ def hostrange(replion_types, relaxase_types, mob_cluster_id, ncbi, lit, ETE3DBTA
         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,database_directory)
+            '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,database_directory)
+        '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,database_directory)
+        '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,database_directory)
-        heir = getHeirarchy(taxid,ETE3DBTAXAFILE,database_directory)
+        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']
 
@@ -949,7 +949,7 @@ def determine_mpf_type(hits):
     return max(types, key=lambda i: types[i])
 
 
-def build_mobtyper_report(plasmid_contig_info, out_dir, outfile, seq_dict, ncbi, lit,ETE3DBTAXAFILE):
+def build_mobtyper_report(plasmid_contig_info, out_dir, outfile, seq_dict, ncbi, lit, ETE3DBTAXAFILE, database_directory):
     mob_typer_results = {}
     for clust_id in plasmid_contig_info:
 
@@ -1064,7 +1064,7 @@ def build_mobtyper_report(plasmid_contig_info, out_dir, outfile, seq_dict, ncbi,
         else:
             mob_cluster_id = '-'
 
-        host_range = hostrange(rep_types, relaxase_types, mob_cluster_id, ncbi, lit,ETE3DBTAXAFILE)
+        host_range = hostrange(rep_types, relaxase_types, mob_cluster_id, ncbi, lit, ETE3DBTAXAFILE, database_directory)
 
         for field in host_range:
             mob_typer_results[clust_id][field] = host_range[field]

diff --git a/mob_suite/version.py b/mob_suite/version.py
@@ -1,2 +1 @@
-__version__ = '3.1.5'
-
+__version__ = '3.1.6'