Create a class to handle mapping extension to ucsc view attributes.

[htsworkflow.git] / extra / ucsc_encode_submission / test_ucsc_gather.py

diff --git a/extra/ucsc_encode_submission/test_ucsc_gather.py b/extra/ucsc_encode_submission/test_ucsc_gather.py
new file mode 100644 (file)
index 0000000..64f712d
--- /dev/null
+++ b/extra/ucsc_encode_submission/test_ucsc_gather.py
@@ -0,0 +1,74 @@
+import unittest
+
+import ucsc_gather
+
+class testUCSCGather(unittest.TestCase):
+    def test_view_attribute_map(self):
+        view_map = ucsc_gather.NameToViewMap()
+        view_map.lib_cache["0"] = {
+            "cell_line": "NLHF",
+            "replicate": "1",
+            "lane_set": {},
+            }
+    
+        a = view_map.find_attributes("foo.ini", "0")    
+        self.failUnless(a["view"] is None)
+    
+        a = view_map.find_attributes("asdf.fdsa", "0")
+        self.failUnless(a is None)
+    
+        a = view_map.find_attributes("foo.fastq", "0")
+        self.failUnlessEqual(a["view"], "Fastq", "0")
+    
+        a = view_map.find_attributes("foo_r1.fastq", "0")
+        self.failUnlessEqual(a["view"], "FastqRd1", "0")
+
+    def test_get_library_info_paired(self):
+        view_map = ucsc_gather.NameToViewMap()
+        view_map.lib_cache["11588"] = {
+            u'antibody_id': None,
+            u'cell_line': u'NHLF',
+            u'cell_line_id': 13,
+            u'experiment_type': u'RNA-seq',
+            u'experiment_type_id': 4,
+            u'gel_cut_size': 300,
+            u'hidden': False,
+            u'id': u'11588',
+            u'insert_size': 200,
+            u'lane_set': [{u'flowcell': u'61PKCAAXX',
+                           u'lane_number': 8,
+                           u'paired_end': True,
+                           u'read_length': 76,
+                           u'status': u'Unknown',
+                           u'status_code': None},
+                          {u'flowcell': u'61PKLAAXX',
+                           u'lane_number': 8,
+                           u'paired_end': True,
+                           u'read_length': 76,
+                           u'status': u'Unknown',
+                           u'status_code': None}],
+            u'library_id': u'11588',
+            u'library_name': u'Paired ends 254 NHLF 31',
+            u'library_species': u'Homo sapiens',
+            u'library_species_id': 8,
+            u'library_type': u'Paired End',
+            u'library_type_id': 2,
+            u'made_by': u'Brian',
+            u'made_for': u'Brian',
+            u'notes': u'300 bp gel fragment, SPRI beads cleanup',
+            u'replicate': 2,
+            u'stopping_point': u'1Aa',
+            u'successful_pM': None,
+            u'undiluted_concentration': u'26.2'}
+
+        a = view_map.find_attributes("foo.bam", "11588")
+        self.failUnlessEqual(a["view"], "Paired")
+        self.failUnlessEqual(a["insertLength"], 200)
+
+
+def suite():
+    return unittest.makeSuite(testUCSCGather,"test")
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")
+