Merge pull request #13 from andrewjpage/verbose

Species list bug

VERSION

@@ -1 +1 @@
-2.1.6
+2.1.7

scripts/socru_species

@@ -23,4 +23,4 @@ parser.add_argument('--version', action='version', version=str(version))
 
 options = parser.parse_args()
 
-Schemas().print_all()
+Schemas(options.verbose).print_all()

socru/Fasta.py

@@ -38,6 +38,8 @@ def largest_contig_check(self, largest_contig, record):
     def calc_fragment_coords(self, boundries):
         genome_length = len(self.chromosome.seq)
         fragments = []
+        if not boundries:
+            return []
 
         start_coord = 0
         end_coord = genome_length

socru/Socru.py

@@ -107,6 +107,8 @@ def write_novel_profile_to_file(self, tg, type_output_string):
     # refactor
     def run_analysis(self, input_file, p, d):
         boundries = self.find_rrna_boundries(input_file)
+        if not boundries:
+            return ''
         fragments = self.populate_fragments_from_chromosome(input_file, boundries)
 
         tmpdir = mkdtemp()

socru/tests/Socru_test.py

@@ -32,9 +32,19 @@ def test_socru_valid(self):
         self.assertTrue(os.path.exists('output_file'))
         self.assertTrue(os.path.exists('blast'))
 
-        os.remove('blast')
-        os.remove('output_file')
-        os.remove('novel')
-        os.remove('newfrag.fa')
-        os.remove('output_plot.png')
+        for file_name in ['blast', 'output_file', 'newfrag.fa', 'output_plot.png', 'novel']:
+            if os.path.exists(file_name):
+                os.remove(file_name)
+
+    def test_operon_wrapped_around_ends(self):
+		# If there is no operon identified, then skip and dont throw an error
+        g = Socru(TestOptions([os.path.join(data_dir, 'wrapped.fa')], 'Salmonella_enterica', None, 1000,1000,1, 'output_file', False, 'novel', 'newfrag.fa', None, 'blast', 'output_plot.png'))
+        g.run()
+        self.assertTrue(os.path.exists('output_file'))
+        self.assertTrue(os.path.exists('blast'))
+
+        for file_name in ['blast', 'output_file', 'newfrag.fa', 'output_plot.png', 'novel']:
+            if os.path.exists(file_name):
+                os.remove(file_name)
+