updated filetypes and added tests

fluff/track.py

@@ -231,7 +231,7 @@ def __init__(self, fname, **kwargs):
         self.rmrepeats = kwargs.get("rmrepeats", False)
         self.fragmentsize = kwargs.get("fragmentsize", None)
 
-        if fname.endswith("bam"):
+        if fname.split(".")[-1] in self._filetypes:
             self.track = pysam.AlignmentFile(fname, "rb")
             self.ftype = "bam"
             self.chroms = self.track.references
@@ -644,7 +644,7 @@ class WigTrack(Track):
     def __init__(self, fname, **kwargs):
         self.fname = fname
 
-        if fname.endswith("bg") or fname.endswith("wig"):
+        if fname.split(".")[-1] in self._filetypes:
             self.track = pybedtools.BedTool(fname)
             self.ftype = "wig"
         else:
@@ -749,7 +749,7 @@ class BigWigTrack(Track):
     _filetypes = ["bw", "bigWig"]
 
     def __init__(self, fname, **kwargs):
-        if fname.endswith("bw"):
+        if fname.split(".")[-1] in self._filetypes:
             self.track = pyBigWig.open(fname)
             self.ftype = "bw"
         else:

tests/data/profile.bedGraph

@@ -0,0 +1,16 @@
+scaffold_1	14750061	14750067	1
+scaffold_1	44749422	44749429	1
+scaffold_1	44749429	44749457	2
+scaffold_1	44749457	44749464	1
+scaffold_1	44749713	44749748	1
+scaffold_1	44749845	44749868	1
+scaffold_1	44749868	44749880	2
+scaffold_1	44749880	44749903	1
+scaffold_1	44749934	44749938	1
+scaffold_1	44749938	44749969	2
+scaffold_1	44749969	44749973	1
+scaffold_1	44749994	44750026	1
+scaffold_1	44750026	44750029	2
+scaffold_1	44750029	44750032	1
+scaffold_1	44750032	44750061	2
+scaffold_1	44750061	44750067	1

tests/test_track.py

@@ -3,7 +3,7 @@
 
 @pytest.fixture
 def tracks():
-    ftypes = ["bam", "bed", "wig", "bg", "bw", "wig.gz", "bg.gz"]#, "bed.gz"]
+    ftypes = ["bam", "bed", "wig", "bg", "bw", "wig.gz", "bg.gz", "bigWig", "bedGraph"]#, "bed.gz"]
     my_tracks = []
     for ftype in ftypes:
         fname = "tests/data/profile." + ftype