diff tests/test_riboplot.py @ 7:096c6bbf4a04

Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments

--- a/tests/test_riboplot.py	Wed Aug 12 16:28:43 2015 +0100
+++ b/tests/test_riboplot.py	Thu Aug 13 15:03:20 2015 +0100
@@ -27,7 +27,7 @@
             ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE])
         save_path = os.environ['PATH']
         os.environ['PATH'] = ''
-        self.assertRaises(OSError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file)
+        self.assertRaises(OSError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file)
         os.environ['PATH'] = save_path
 
     def test_is_bam_valid(self):
@@ -70,19 +70,19 @@
         args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                        '-l', '-1'])  # invalid read length -1
         self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
-                          args.ribo_file, None, args.read_length)
+                          ribo_file=args.ribo_file, read_length=args.read_length)
 
         args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                        '-l', '100'])  # invalid read length 100
         self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
-                          args.ribo_file, None, args.read_length)
+                          ribo_file=args.ribo_file, read_length=args.read_length)
 
     def test_valid_read_offset(self):
         """Read offset should be positive."""
         args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME,
                                        '-s', '-1'])  # invalid read offset -1
         self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments,
-                          args.ribo_file, None, None, args.read_offset)
+                          ribo_file=args.ribo_file, read_offset=args.read_offset)
 
     def test_is_fasta_valid(self):
         """A valid FASTA file can be opened with pysam.FastaFile."""
@@ -116,7 +116,7 @@
         # using transcriptome FASTA file as the invalid RNA file for test
         parser = riboplot.create_parser()
         args = parser.parse_args(['-b', RIBO_FILE,  '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA])
-        self.assertRaises(ValueError, ribocore.check_optional_arguments, args.ribo_file, args.rna_file)
+        self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file)
 
 class RiboPlotTestCase(unittest.TestCase):