fixes to fastq counting and test function names

broadinstitute · Jun 16, 2016 · 0fc1c09 · 0fc1c09
1 parent ac5cf6d
commit 0fc1c09
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/assembly.py b/assembly.py
@@ -55,8 +55,9 @@ def __init__(self, n_start, n_trimmed, n_rmdup, n_purge, n_subsamp):
 
 
 def count_fastq_reads(inFastq):
+    ''' Maybe move this to util.file one day '''
     with util.file.open_or_gzopen(inFastq, 'rt') as inf:
-        n = sum(1 for line in inf if line.startswith('>'))
+        n = sum(1 for line in inf if line.startswith('@'))
     return n
 
 

diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -57,7 +57,7 @@ def test_empty_input_succeed(self):
         self.assertEqual(os.path.getsize(outFasta), 0)
         os.unlink(outFasta)
 
-    def test_empty_input_succeed(self):
+    def test_empty_input_fail(self):
         inDir = util.file.get_test_input_path()
         inBam = os.path.join(inDir, 'empty.bam')
         clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')