Address some warnings.

geronimp · Sep 29, 2023 · a2b19c0 · a2b19c0
1 parent 02e508a
commit a2b19c0
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/graftm/expand_searcher.py b/graftm/expand_searcher.py
@@ -125,7 +125,7 @@ def generate_expand_search_database_from_contigs(self, contig_files, output_data
                     if len(seqio.read_fasta_file(orfs.name)) <= 1:# Just to build on this, you need to check if there is > 1 hit
                                                                   # otherwise mafft will fail to align, causing a crash when hmmbuild is
                                                                   # run on an empty file.
-                        logging.warn("Failed to find two or more matching ORFs in the expand_search contigs")
+                        logging.warning("Failed to find two or more matching ORFs in the expand_search contigs")
                         return False
 
                     # Run mafft to align them

diff --git a/test/test_graft.py b/test/test_graft.py
@@ -1239,7 +1239,7 @@ def test_forward_and_reverse_slash_type_fastq(self):
         fwd = '''@FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/1
 ACACTGCCCAGACACCTACGGGTGGCTGCAGTCGAGGATCTTCGGCAATGGGCGAAAGCCTGACCGAGCGACGCCGCGTGTGGGATGAAGGCCCTCGGGT
 +
-^^_cccacgeecafgfghhhhheYea_c^efaff`eggfhhhhf]`_d]]X^aa\]^Y^a`[^bbaZaaaa]]a]_[]HTX`[[[_[]`_][`^^`]__a
+^^_cccacgeecafgfghhhhheYea_c^efaff`eggfhhhhf]`_d]]X^aa\\]^Y^a`[^bbaZaaaa]]a]_[]HTX`[[[_[]`_][`^^`]__a
 '''
         rev = '''@FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/2
 CGGGGTATCTAATCCCGTTCGCTCCCCTAGCTTTCGTGCCTCAGCGTCAGAAAAGACCCAGTGAGCCGCTTTCGCCCCCGGTGTTCCTTAGGATATCAAC

diff --git a/test/test_taxonomy_extractor.py b/test/test_taxonomy_extractor.py
@@ -36,22 +36,22 @@
 class Tests(unittest.TestCase):
 
     def test_hello_world(self):
-        self.assertEquals({u'a': [],
+        self.assertEqual({u'a': [],
                            u'b': [u't1'],
                            u'c': [u't1']},
                           TaxonomyExtractor().taxonomy_from_annotated_tree(\
                             Tree.get(data="(a,(b,c)'t1':0.9)root;", schema='newick')))
 
     def test_bootstraps_in_annotated_tree(self):
-        self.assertEquals({u'a': [],
+        self.assertEqual({u'a': [],
                            u'b': [u't1'],
                            u'c': [u't1']},
                           TaxonomyExtractor().taxonomy_from_annotated_tree(\
                             Tree.get(data="(a,(b,c)'0.01973:t1':0.9)root;", schema='newick')))
 
 
     def test_bootstraps_in_annotated_tree_alongside_empty_taxa(self):
-        self.assertEquals({u'a': [],
+        self.assertEqual({u'a': [],
                            u'b': [],
                            u'c': ['tax'],
                            u'd': ['tax']},