erange version 4.0a dev release

[erange.git] / test / testCommoncode.py

diff --git a/test/testCommoncode.py b/test/testCommoncode.py
index 1ea4f803c2a7dcd7357dff35995d19ca357728a9..43eb96bc2a3153e7cbf0bb5719fa13320195512c 100644 (file)
--- a/test/testCommoncode.py
+++ b/test/testCommoncode.py
@@ -7,7 +7,7 @@ import unittest
 import os
 import string
 from array import array
-from Erange import commoncode
+from erange import commoncode
 from cistematic.genomes import Genome
 
 
@@ -277,7 +277,7 @@ class TestCommoncode(unittest.TestCase):
         result = ([], 0.0, array("f"), 0.0)
         self.assertEquals(result, commoncode.findPeak(hitList, 0, 0))
 
-        hitList= [[4, "+", 0.5]]
+        hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
         result = ([6, 7], 1.0, array("f", [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), 1.0)
         self.assertEquals(result, commoncode.findPeak(hitList, 0, 10))
         result = ([6, 7], 0.5, array('f', [0.0, 0.0, 0.0555555559694767, 0.1666666716337204, 0.3333333432674408, 0.4444444477558136, 0.5, 0.5, 0.0, 0.0]), 0.5)
@@ -287,11 +287,11 @@ class TestCommoncode(unittest.TestCase):
         result = ([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], 0.0, array("f", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), 0.0, 6)
         self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, shift="auto", returnShift=True))
 
-        hitList= [[4, "+", 0.5]]
+        hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
         result = ([7], 1.0, array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), 1.0, 3)
         self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, shift=3, returnShift=True))
 
-        hitList= [[4, "+", 0.5]]
+        hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
         result = ([6, 7], 1.0, array('f', [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), 1.0, 1.0)
         self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, leftPlus=True))
         result = ([7], 1.0, array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), 1.0, 1.0, 3)
@@ -300,12 +300,26 @@ class TestCommoncode(unittest.TestCase):
 
     #TODO: write test
     def testGetBestShiftForRegion(self):
-        hitList = [[14, "-", 1.0], [16, "-", 1.0], [24, "+", 1.0],  [26, "+", 10.0]]
+        hitList = [{"start": 14, "sense": "-", "weight": 1.0},
+                   {"start": 16, "sense": "-", "weight": 1.0},
+                   {"start": 24, "sense": "+", "weight": 1.0},
+                   {"start": 26, "sense": "+", "weight": 10.0}
+        ]
         self.assertEquals(74, commoncode.getBestShiftForRegion(hitList, 0, 100))
         self.assertEquals(16, commoncode.getBestShiftForRegion(hitList, 0, 100, maxShift=30))
         self.assertEquals(0, commoncode.getBestShiftForRegion(hitList, 0, 100, maxShift=10))
 
 
+    #TODO: write test
+    def testFindPeakSequenceArray(self):
+        pass
+
+
+    #TODO: write test
+    def testGetPeakPositionList(self):
+        pass
+
+
     #TODO: write test
     def testGetFeaturesByChromDict(self):
         firstFeatures = {"I": (4123, 4219, "Y74C9A.3", "R", "3UTR"),
@@ -396,42 +410,42 @@ class TestCommoncode(unittest.TestCase):
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[1, "+", 1.0]]}
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]}
         result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")],
                               "2": [("regionID2", 1, 1000, 1000, "F")]
         }
-        hitDict = {"1": [[1, "+", 1.0]],
-                   "2": [[1, "+", 1.0]]
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}],
+                   "2": [{"start": 1, "sense": "+", "weight": 1.0}]
         }
         result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [80, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}]}
         result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [80, "+", 0.5], [15, "+", 1.0]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}, {"start": 15, "sense": "+", "weight": 1.0}]}
         result = ({"regionID": [2.0, 0.0, 0.0, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [80, "+", 0.5], [200, "+", 2.0]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 80, "sense": "+", "weight": 0.5}, {"start": 200, "sense": "+", "weight": 2.0}]}
         result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[1, "+", 1.0]]}
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]}
         regionList = ["regionID"]
         result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[1, "+", 1.0]]}
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]}
         regionList = ["empty region"]
         result = ({"empty region": [0.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList))
@@ -439,8 +453,8 @@ class TestCommoncode(unittest.TestCase):
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")],
                               "2": [("regionID2", 1, 1000, 1000, "F")]
         }
-        hitDict = {"1": [[1, "+", 1.0]],
-                   "2": [[1, "+", 1.0]]
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}],
+                   "2": [{"start": 1, "sense": "+", "weight": 1.0}]
         }
         regionList = ["regionID", "regionID2"]
         result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100})
@@ -449,8 +463,8 @@ class TestCommoncode(unittest.TestCase):
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")],
                               "2": [("regionID2", 1, 1000, 1000, "F")]
         }
-        hitDict = {"1": [[1, "+", 1.0]],
-                   "2": [[1, "+", 1.0]]
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}],
+                   "2": [{"start": 1, "sense": "+", "weight": 1.0}]
         }
         regionList = ["empty region", "regionID2"]
         result = ({"regionID2": [1.0, 0.0, 0.0, 0.0], "empty region": [0.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100})
@@ -459,73 +473,73 @@ class TestCommoncode(unittest.TestCase):
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")],
                               "2": [("regionID2", 1, 1000, 1000, "F")]
         }
-        hitDict = {"1": [[1, "+", 1.0]],
-                   "2": [[1, "+", 1.0]]
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}],
+                   "2": [{"start": 1, "sense": "+", "weight": 1.0}]
         }
         regionList = ["regionID2"]
         result = ({"regionID2": [1.0, 0.0, 0.0, 0.0]}, {"regionID2": 1000, "regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, regionList))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[1, "+", 1.0]]}
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]}
         result = ({"regionID": [2.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, normalizedTag=2.0))
 
         regionsByChromDict = {"1": [(1, 100, "regionID", 100, "F")]}
-        hitDict = {"1": [[1, "+", 1.0]]}
+        hitDict = {"1": [{"start": 1, "sense": "+", "weight": 1.0}]}
         result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, defaultRegionFormat=False))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}]}
         fixedFirstBin = 20
         result = ({"regionID": [1.0, 0.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}]}
         fixedFirstBin = 5
         result = ({"regionID": [0.0, 1.0, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]}
         fixedFirstBin = 20
         result = ({"regionID": [1.0, 0.5, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[80, "+", 1.0], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 80, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]}
         fixedFirstBin = 5
         result = ({"regionID": [0.0, 1.5, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, fixedFirstBin=fixedFirstBin))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]}
         binLength = 25
         result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]}
         binLength = 50
         result = ({"regionID": [1.0, 0.5, 0.0, 0.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 85, "sense": "+", "weight": 0.5}]}
         binLength = 15
         result = ({"regionID": [1.0, 0.0, 0.0, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "F")]}
-        hitDict = {"1": [[10, "+", 1.0], [40, "+", 0.7], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 40, "sense": "+", "weight": 0.7}, {"start": 85, "sense": "+", "weight": 0.5}]}
         binLength = 15
         result = ({"regionID": [1.0, 0.0, 0.7, 0.5]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen, binLength=binLength))
 
         regionsByChromDict = {"1": [("regionID", 1, 100, 100, "R")]}
-        hitDict = {"1": [[10, "+", 1.0], [40, "+", 0.7], [85, "+", 0.5]]}
+        hitDict = {"1": [{"start": 10, "sense": "+", "weight": 1.0}, {"start": 40, "sense": "+", "weight": 0.7}, {"start": 85, "sense": "+", "weight": 0.5}]}
         result = ({"regionID": [0.5, 0.0, 0.7, 1.0]}, {"regionID": 100})
         self.assertEquals(result, commoncode.computeRegionBins(regionsByChromDict, hitDict, bins, readlen))
         result = ({"regionID": [0.5, 0.0, 0.7, 1.0]}, {"regionID": 100})