Merge commit 'upstream/0.3.1'

[pysam.git] / tests / pysam_test.py

diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index 5be5ca4c783f74cef3ebf775681ef1f95a619269..aefcbb94e2a60fcdd651ae7695c2e22d9834952e 100755 (executable)
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -100,11 +100,17 @@ class BinaryTest(unittest.TestCase):
                 ("ex1.view", "samtools view ex1.bam > ex1.view"),
                 ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ),
                 ),
+          "view2" :
+        (
+                ("ex1.view", "samtools view -bT ex1.fa -o ex1.view2 ex1.sam"),
+                # note that -o ex1.view2 throws exception.
+                ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ),
+                ),
         }
 
     # some tests depend on others. The order specifies in which order
     # the samtools commands are executed.
-    mOrder = ('faidx', 'import', 'index', 'pileup1', 'pileup2', 'glfview', 'view' )
+    mOrder = ('faidx', 'import', 'index', 'pileup1', 'pileup2', 'glfview', 'view', 'view2' )
 
     def setUp( self ):
         '''setup tests. 
@@ -247,11 +253,22 @@ class IOTest(unittest.TestCase):
         samfile.close()
         self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120)
 
-    def testPileupFromClosedFile( self ):
+    def testClosedFile( self ):
+        '''test that access to a closed samfile raises ValueError.'''
 
         samfile = pysam.Samfile( "ex1.bam", "rb" )
         samfile.close()
+        self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120)
         self.assertRaises( ValueError, samfile.pileup, 'chr1', 100, 120)
+        self.assertRaises( ValueError, samfile.getrname, 0 )
+        self.assertRaises( ValueError, samfile.tell )
+        self.assertRaises( ValueError, samfile.write, None )
+        self.assertRaises( ValueError, samfile.seek, 0 )
+        self.assertRaises( ValueError, getattr, samfile, "nreferences" )
+        self.assertRaises( ValueError, getattr, samfile, "references" )
+        self.assertRaises( ValueError, getattr, samfile, "lengths" )
+        self.assertRaises( ValueError, getattr, samfile, "text" )
+        self.assertRaises( ValueError, getattr, samfile, "header" )
 
     def testBinaryReadFromSamfile( self ):
         pass
@@ -267,12 +284,6 @@ class IOTest(unittest.TestCase):
         self.assertRaises( ValueError, samfile.fetch )
         self.assertEqual( len(list( samfile.fetch(until_eof = True) )), 3270 )
 
-    def testReadingFromFileWithWrongMode( self ):
-
-        assert not os.path.exists( "ex2.bam.bai" )
-        samfile = pysam.Samfile( "ex2.bam", "r" )
-        self.assertRaises( ValueError, samfile.fetch )
-
 class TestIteratorRow(unittest.TestCase):
 
     def setUp(self):
@@ -602,9 +613,29 @@ class TestExceptions(unittest.TestCase):
     def testOutOfRangeLargeOldFormat(self):
         self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" )
 
+    def testZeroToZero(self):        
+        '''see issue 44'''
+        self.assertEqual( len(list(self.samfile.fetch('chr1', 0, 0))), 0)
+
     def tearDown(self):
         self.samfile.close()
 
+
+class TestWrongFormat(unittest.TestCase):
+    '''test cases for opening files not in bam/sam format.'''
+
+    def testOpenSamAsBam( self ):
+        self.assertRaises( ValueError, pysam.Samfile, 'ex1.sam', 'rb' )
+
+    def testOpenBamAsSam( self ):
+        self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' )
+
+    def testOpenFastaAsSam( self ):
+        self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' )
+
+    def testOpenFastaAsBam( self ):
+        self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'rb' )
+
 class TestFastaFile(unittest.TestCase):
 
     mSequences = { 'chr1' :
@@ -691,7 +722,7 @@ class TestAlignedRead(unittest.TestCase):
         a.mpos=200
         a.isize=167
        a.qual="1234" * 3
-
+        # todo: create tags
         return a
 
     def testUpdate( self ):
@@ -760,6 +791,19 @@ class TestAlignedRead(unittest.TestCase):
 
         return a
 
+    def testTagParsing( self ):
+        '''test for tag parsing
+
+        see http://groups.google.com/group/pysam-user-group/browse_thread/thread/67ca204059ea465a
+        '''
+        samfile=pysam.Samfile( "ex8.bam","rb" )
+
+        for entry in samfile:
+            before = entry.tags
+            entry.tags = entry.tags
+            after = entry.tags
+            self.assertEqual( after, before )
+
 class TestDeNovoConstruction(unittest.TestCase):
     '''check BAM/SAM file construction using ex3.sam
     
@@ -874,6 +918,7 @@ class TestDeNovoConstruction(unittest.TestCase):
         
         os.unlink( tmpfilename )
 
+
 class TestDoubleFetch(unittest.TestCase):
     '''check if two iterators on the same bamfile are independent.'''