fixed search taxa list when using --coreTaxa

fdog/libs/orthosearch.py

@@ -278,3 +278,34 @@ def run_hamstr(args):
 
     ### return
     return({**{seed_id_mod:seed_seq}, **hamstr_out})
+
+
+def get_search_taxa_ids(searchTaxa, searchpath):
+    """ Get taxonomy IDs for search taxa
+    Either from searchTaxa_dir, or from user input list (--searchTaxa)
+    Return dictionary {taxID:<TaxName>@<TaxID>@Ver}
+    """
+    tax_ids = {}
+    if not searchTaxa == '' and not len(searchTaxa) == 0:
+        ignored_taxa = []
+        if os.path.exists(os.path.abspath(searchTaxa)):
+            search_taxa = general_fn.read_file(searchTaxa)
+        else:
+            search_taxa = searchTaxa.split(',')
+
+        for search_taxon in search_taxa:
+            if not os.path.exists(
+                    os.path.abspath(
+                        '%s/%s/%s.fa' % (searchpath,search_taxon,search_taxon))):
+                ignored_taxa.append(search_taxon)
+            else:
+                id = search_taxon.split('@')[1]
+                if not id in tax_ids:
+                    tax_ids[id] = search_taxon
+        if len(ignored_taxa) > 0:
+            print(
+                'WARNING: %s taxa cannot be found at %s\n%s'
+                % (len(ignored_taxa), searchpath, ignored_taxa))
+    else:
+        tax_ids = general_fn.get_ids_from_folder(searchpath, 'searchTaxa_dir')
+    return(tax_ids)

fdog/runMulti.py

@@ -350,6 +350,8 @@ def main():
         check_fas = fas_fn.check_fas_executable()
         if check_fas == 0:
             sys.exit('ERROR: FAS is not executable! You still can use fDOG with --fasOff!')
+    check_time = time.time()
+    print('==> Preparation finished in ' + '{:5.3f}s'.format(check_time - begin))
 
     ### START
     Path(outpath).mkdir(parents=True, exist_ok=True)
@@ -401,7 +403,7 @@ def main():
                     exit('ERROR: Taxon group "%s" invalid!' % group)
                 ### create taxonomy tree from list of search taxa
                 searchTaxa = []
-                tax_ids = core_fn.get_core_taxa_ids(coreTaxa, corepath)
+                tax_ids = ortho_fn.get_search_taxa_ids(searchTaxa, searchpath)
 
                 for tax_id in tax_ids.keys():
                     check = tree_fn.check_taxon_group(group_id[group][0], tax_id, ncbi)

fdog/runSingle.py

@@ -225,6 +225,8 @@ def main():
         check_fas = fas_fn.check_fas_executable()
         if check_fas == 0:
             sys.exit('ERROR: FAS is not executable! You still can use fDOG with --fasOff!')
+    check_time = time.time()
+    print('==> Preparation finished in ' + '{:5.3f}s'.format(check_time - begin))
 
     ##### Identify seed ID from refspec genome
     if reuseCore:
@@ -265,7 +267,7 @@ def main():
                 exit('ERROR: Taxon group "%s" invalid!' % group)
             ### create taxonomy tree from list of search taxa
             searchTaxa = []
-            tax_ids = core_fn.get_core_taxa_ids(coreTaxa, corepath)
+            tax_ids = ortho_fn.get_search_taxa_ids(searchTaxa, searchpath)
 
             for tax_id in tax_ids.keys():
                 check = tree_fn.check_taxon_group(group_id[group][0], tax_id, ncbi)

setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="fdog",
-    version="0.1.26",
+    version="0.1.27",
     python_requires='>=3.7.0',
     description="Feature-aware Directed OrtholoG search tool",
     long_description=long_description,