Merge github.com:broadinstitute/viral-ngs into sy-pytest

pipes/config.yaml

@@ -37,6 +37,9 @@ kraken_db: "/idi/sabeti-scratch/yesimon/db/kraken_full_20150910"
 # Path of DIAMOND database file for metagenomics identification
 diamond_db: "/idi/sabeti-scratch/yesimon/db/diamond_db/nr"
 
+# Directory of the krona database for generating html reports.
+krona_db: "/idi/sabeti-scratch/yesimon/db/krona"
+
 # These are variables that must be set
 env_vars:
   # The directory path to the location of the GATK jar file.

pipes/rules/metagenomics.rules

@@ -36,7 +36,7 @@ rule krona_import_taxonomy:
     output: join(config["data_dir"], config["subdirs"]["metagenomics"], "{sample}.kraken.krona.html")
     shell:
         """
-        {config[bin_dir]}/metagenomics.py krona {input} {output} --noRank
+        {config[bin_dir]}/metagenomics.py krona {input} {config[krona_db]} {output} --noRank
         """
 
 

test/integration/test_kraken.py

@@ -87,10 +87,14 @@ class CommonTests(object):
     @unittest.skipIf(sys.version_info < (3,2), "Python version is too old for snakemake.")
     def test_pipes(self):
         runner = SnakemakeRunner()
-        runner.set_override_config({
+        override_config = {
             'kraken_db': self.db,
             'diamond_db': None,
-        })
+        }
+        krona_db =  getattr(self, 'krona_db', None)
+        if krona_db:
+            override_config['krona_db'] = self.krona_db
+        runner.set_override_config(override_config)
         runner.setup()
         runner.link_samples([self.bam], destination='source')
         runner.create_sample_files(sample_files=['samples_metagenomics'])
@@ -101,10 +105,10 @@ def test_pipes(self):
         krona_out = join(runner.workdir, runner.data_dir, runner.config['subdirs']['metagenomics'],
                              '.'.join([os.path.splitext(os.path.basename(self.bam))[0], 'kraken.krona.html']))
 
-        # runner.run(['all_metagenomics'])
-        runner.run([kraken_out])
+        runner.run(['all_metagenomics'])
+        # runner.run([kraken_out])
         self.assertGreater(os.path.getsize(kraken_out), 0)
-        # self.assertGreater(os.path.getsize(krona_out), 0)
+        self.assertGreater(os.path.getsize(krona_out), 0)
 
     def test_kraken(self):
         bin = join(util.file.get_project_path(), 'metagenomics.py')
@@ -119,10 +123,12 @@ def test_kraken(self):
         self.assertGreater(os.path.getsize(out_reads), 0)
 
 
-class TestKrakenTiny(TestKrakenBase, CommonTests):
+class TestKrakenTiny(TestKrakenBase, TestKronaBase, CommonTests):
 
     @classmethod
     def setUpClass(cls):
+        TestKronaBase.setUpClass()
+        cls.krona_db = cls.build_krona_db()
         super().setUpClass()
         cls.data_dir = join(util.file.get_test_input_path(), 'TestToolKraken')
         cls.db_dir = os.path.join(cls.data_dir, 'db')
@@ -147,10 +153,12 @@ def test_kraken_tool(self):
         self.assertGreater(os.path.getsize(out_report), 0)
         self.assertGreater(os.path.getsize(out_filtered), 0)
 
-class TestKrakenVirusMix(TestKrakenBase, CommonTests):
+class TestKrakenVirusMix(TestKrakenBase, TestKronaBase, CommonTests):
 
     @classmethod
     def setUpClass(cls):
+        TestKronaBase.setUpClass()
+        cls.krona_db = cls.build_krona_db()
         super().setUpClass()
         cls.data_dir = join(util.file.get_test_input_path(), 'TestKrakenViralMix')
         cls.db_dir = os.path.join(cls.data_dir, 'db')

util/misc.py

@@ -216,7 +216,7 @@ def run_and_print(args, stdout=None, stderr=None,
                     print(e.output.decode('utf-8'))
                     try:
                         print(e.stderr.decode('utf-8'))
-                    except TypeError:
+                    except AttributeError:
                         pass
                     sys.stdout.flush()
                 raise(e)