added more unit tests

clipper/__init__.py

@@ -0,0 +1,32 @@
+import os
+
+def data_dir():
+    """
+    Returns the data directory that contains files for data and
+    documentation.
+    """
+    return os.path.join(os.path.dirname(__file__), 'data')
+
+
+def test_dir():
+
+    """
+    Returns the data directory that contains example files for tests and
+    documentation.
+    """
+    return os.path.join(os.path.dirname(__file__), 'test')
+
+def data_file(fn):
+    fn = os.path.join(data_dir(), fn)
+
+    if not os.path.exists(fn):
+        raise ValueError("%s does not exist")
+    return fn
+
+
+def test_file(fn):
+    fn = os.path.join(data_dir(), fn)
+
+    if not os.path.exists(fn):
+        raise ValueError("%s does not exist")
+    return fn

clipper/data/test.AS.STRUCTURE_mRNA.lengths

@@ -0,0 +1,5 @@
+ENSG00000232113	384
+ENSG00000228150	323
+ENSG00000223883	437
+ENSG00000135750	3141
+ENSG00000227280	212

clipper/data/test.AS.STRUCTURE_premRNA.lengths

@@ -0,0 +1,5 @@
+ENSG00000232113	1147
+ENSG00000228150	3088
+ENSG00000223883	46051
+ENSG00000135750	35997
+ENSG00000227280	609

clipper/src/call_peak.py

@@ -315,7 +315,7 @@ def call_peaks(loc, gene_length, bam_fileobj=None, bam_file=None,
     """
 
     #setup
-    chrom, gene_name, tx_start, tx_end, signstrand = loc.split("|")
+    chrom, gene_name, tx_start, tx_end, signstrand = loc
 
 
     #logic reading bam files
@@ -436,7 +436,7 @@ def peaks_from_info(wiggle, pos_counts, lengths, loc, gene_length,
     #peak_dict['loc'] = loc
 
     #data munging
-    chrom, gene_name, tx_start, tx_end, signstrand = loc.split("|")
+    chrom, gene_name, tx_start, tx_end, signstrand = loc
     tx_start, tx_end = map(int, [tx_start, tx_end])    
 
     #used for poisson calclulation?