import os
import string
from array import array
-from Erange import commoncode
+from erange import commoncode
+from erange import Region
from cistematic.genomes import Genome
regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t")
testfile.write(regionEntry)
testfile.close()
- result = {"1": [(10, 20, 10)]}
- self.assertEquals(result, commoncode.getMergedRegions("regionTestFile"))
+ result = commoncode.getMergedRegions("regionTestFile")
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
os.remove("regionTestFile")
regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t")
regionList = [regionEntry]
- result = {"1": [(10, 20, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList))
- result = {"1": [(5, 25, 20)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, pad=5))
- result = {"1": [(12, 18, 6)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, pad=-2))
- result = {"chr1": [(10, 20, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, fullChrom=True))
+ result = commoncode.getMergedRegionsFromList(regionList)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, pad=5)
+ self.assertEquals(5, result["1"][0].start)
+ self.assertEquals(25, result["1"][0].stop)
+ self.assertEquals(20, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, pad=-2)
+ self.assertEquals(12, result["1"][0].start)
+ self.assertEquals(18, result["1"][0].stop)
+ self.assertEquals(6, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, fullChrom=True)
+ self.assertEquals(10, result["chr1"][0].start)
+ self.assertEquals(20, result["chr1"][0].stop)
+ self.assertEquals(10, result["chr1"][0].length)
regionEntry = string.join(["1", "chr1:10-20", "5"], "\t")
regionList = [regionEntry]
- result = {"1": [(10, 20, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, compact=True, scoreField=2))
+ result = commoncode.getMergedRegionsFromList(regionList, compact=True, scoreField=2)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t")
regionList = [regionEntry]
regionEntry = string.join(["2", "chr1", "15", "40", "10"], "\t")
regionList.append(regionEntry)
- result = {"1": [(10, 40, 30)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList))
- result = {"1": [(10, 20, 10), (15, 40, 25)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, doMerge=False))
- result = {"1": [("1", 10, 20, 10), ("2", 15, 40, 25)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True))
+ result = commoncode.getMergedRegionsFromList(regionList)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(40, result["1"][0].stop)
+ self.assertEquals(30, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, doMerge=False)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(15, result["1"][1].start)
+ self.assertEquals(40, result["1"][1].stop)
+ self.assertEquals(25, result["1"][1].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals("1", result["1"][0].label)
+ self.assertEquals(15, result["1"][1].start)
+ self.assertEquals(40, result["1"][1].stop)
+ self.assertEquals(25, result["1"][1].length)
+ self.assertEquals("2", result["1"][1].label)
regionEntry = string.join(["1", "spacer", "chr1", "10", "20", "5"], "\t")
regionList = [regionEntry]
regionEntry = string.join(["2", "spacer2", "chr1", "15", "40", "10"], "\t")
regionList.append(regionEntry)
- result = {"1": [("1\tspacer", 10, 20, 10), ("2\tspacer2", 15, 40, 25)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True, chromField=2))
+ result = commoncode.getMergedRegionsFromList(regionList, doMerge=False, keepLabel=True, chromField=2)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals("1\tspacer", result["1"][0].label)
+ self.assertEquals(15, result["1"][1].start)
+ self.assertEquals(40, result["1"][1].stop)
+ self.assertEquals(25, result["1"][1].length)
+ self.assertEquals("2\tspacer2", result["1"][1].label)
regionEntry = string.join(["1", "chr1", "10", "20", "5"], "\t")
regionList = [regionEntry]
regionEntry = string.join(["2", "chr1", "2030", "2040", "15"], "\t")
regionList.append(regionEntry)
- result = {"1": [(10, 20, 10), (2030, 2040, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList))
- result = {"1": [(10, 2040, 2030)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, maxDist=3000))
- result = {"1": [(10, 20, 10), (2030, 2040, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, minHits=5))
- result = {"1": [(2030, 2040, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, minHits=12))
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, returnTop=1))
+ result = commoncode.getMergedRegionsFromList(regionList)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(2030, result["1"][1].start)
+ self.assertEquals(2040, result["1"][1].stop)
+ self.assertEquals(10, result["1"][1].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, maxDist=3000)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(2040, result["1"][0].stop)
+ self.assertEquals(2030, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, minHits=5)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(2030, result["1"][1].start)
+ self.assertEquals(2040, result["1"][1].stop)
+ self.assertEquals(10, result["1"][1].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, minHits=12)
+ self.assertEquals(2030, result["1"][0].start)
+ self.assertEquals(2040, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ result = commoncode.getMergedRegionsFromList(regionList, minHits=12)
+ self.assertEquals(2030, result["1"][0].start)
+ self.assertEquals(2040, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
regionEntry = string.join(["1", "chr1", "10", "20", "+", "5"], "\t")
regionList = [regionEntry]
regionEntry = string.join(["2", "chr2", "15", "40", "+", "15"], "\t")
regionList.append(regionEntry)
- result = {"2": [(15, 40, 25)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, scoreField=5, minHits=12))
+ result = commoncode.getMergedRegionsFromList(regionList, scoreField=5, minHits=12)
+ self.assertEquals(15, result["2"][0].start)
+ self.assertEquals(40, result["2"][0].stop)
+ self.assertEquals(25, result["2"][0].length)
self.assertRaises(IndexError, commoncode.getMergedRegionsFromList, regionList, scoreField=6, returnTop=1)
self.assertEquals({}, commoncode.getMergedRegionsFromList(regionList, scoreField=6))
self.assertEquals({}, commoncode.getMergedRegionsFromList(regionList, scoreField=1))
regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40"], "\t")
regionList = [regionEntry]
- result = {"1": [(10, 20, 10)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList))
- result = {"1": [(10, 20, 10, 3, 40)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True))
- result = {"1": [("1", 10, 20, 10, 3, 40)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True))
+ result = commoncode.getMergedRegionsFromList(regionList)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+ self.assertEquals("1", result["1"][0].label)
+
regionEntry = string.join(["2", "chr2", "15", "40", "32", "17"], "\t")
regionList.append(regionEntry)
- result = {"1": [("1", 10, 20, 10, 3, 40)], "2": [("2", 15, 40, 25, 32, 17)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+ self.assertEquals("1", result["1"][0].label)
+ self.assertEquals(15, result["2"][0].start)
+ self.assertEquals(40, result["2"][0].stop)
+ self.assertEquals(25, result["2"][0].length)
+ self.assertEquals(32, result["2"][0].peakPos)
+ self.assertEquals(17, result["2"][0].peakHeight)
+ self.assertEquals("2", result["2"][0].label)
+
regionEntry = string.join(["3", "chr1", "15", "40", "32", "17"], "\t")
regionList.append(regionEntry)
- result = {"1": [("3", 10, 40, 30, 3, 40)], "2": [("2", 15, 40, 25, 32, 17)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(40, result["1"][0].stop)
+ self.assertEquals(30, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+ self.assertEquals("3", result["1"][0].label)
+ self.assertEquals(15, result["2"][0].start)
+ self.assertEquals(40, result["2"][0].stop)
+ self.assertEquals(25, result["2"][0].length)
+ self.assertEquals(32, result["2"][0].peakPos)
+ self.assertEquals(17, result["2"][0].peakHeight)
+ self.assertEquals("2", result["2"][0].label)
+
regionEntry = string.join(["4", "chr2", "65", "88", "72", "7"], "\t")
regionList.append(regionEntry)
- result = {"1": [("3", 10, 40, 30, 3, 40)], "2": [("4", 15, 88, 73, 32, 17)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True))
- result = {"1": [("1", 10, 20, 10, 3, 40), ("3", 15, 40, 25, 32, 17)],
- "2": [("2", 15, 40, 25, 32, 17), ("4", 65, 88, 23, 72, 7)]
- }
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True, doMerge=False))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(40, result["1"][0].stop)
+ self.assertEquals(30, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+ self.assertEquals("3", result["1"][0].label)
+ self.assertEquals(15, result["2"][0].start)
+ self.assertEquals(88, result["2"][0].stop)
+ self.assertEquals(73, result["2"][0].length)
+ self.assertEquals(32, result["2"][0].peakPos)
+ self.assertEquals(17, result["2"][0].peakHeight)
+ self.assertEquals("4", result["2"][0].label)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, keepLabel=True, doMerge=False)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+ self.assertEquals("1", result["1"][0].label)
+ self.assertEquals(15, result["1"][1].start)
+ self.assertEquals(40, result["1"][1].stop)
+ self.assertEquals(25, result["1"][1].length)
+ self.assertEquals(32, result["1"][1].peakPos)
+ self.assertEquals(17, result["1"][1].peakHeight)
+ self.assertEquals("3", result["1"][1].label)
+ self.assertEquals(15, result["2"][0].start)
+ self.assertEquals(40, result["2"][0].stop)
+ self.assertEquals(25, result["2"][0].length)
+ self.assertEquals(32, result["2"][0].peakPos)
+ self.assertEquals(17, result["2"][0].peakHeight)
+ self.assertEquals("2", result["2"][0].label)
+ self.assertEquals(65, result["2"][1].start)
+ self.assertEquals(88, result["2"][1].stop)
+ self.assertEquals(23, result["2"][1].length)
+ self.assertEquals(72, result["2"][1].peakPos)
+ self.assertEquals(7, result["2"][1].peakHeight)
+ self.assertEquals("4", result["2"][1].label)
regionList = ["# comment"]
regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40"], "\t")
regionList.append(regionEntry)
- result = {"1": [(10, 20, 10, 3, 40)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
regionList = ["# pvalue"]
regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value"], "\t")
regionList.append(regionEntry)
- result = {"1": [(10, 20, 10, 3, 40)]}
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True))
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
regionList = ["# readShift"]
regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value"], "\t")
regionList.append(regionEntry)
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True))
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
regionList = ["# pvalue readShift"]
regionEntry = string.join(["1", "chr1", "10", "20", "5", "3", "40", "any value", "any shift"], "\t")
regionList.append(regionEntry)
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True))
- self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1))
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
+ result = commoncode.getMergedRegionsFromList(regionList, keepPeak=True, returnTop=1)
+ self.assertEquals(10, result["1"][0].start)
+ self.assertEquals(20, result["1"][0].stop)
+ self.assertEquals(10, result["1"][0].length)
+ self.assertEquals(3, result["1"][0].peakPos)
+ self.assertEquals(40, result["1"][0].peakHeight)
+
#Test fails - the header line is required if there are fields after the peak which isn't so good
#self.assertEquals(result, commoncode.getMergedRegionsFromList(regionList[1:], keepPeak=True))
#TODO: write test
def testFindPeak(self):
hitList = []
- result = ([], 0.0, array("f"), 0.0)
- self.assertEquals(result, commoncode.findPeak(hitList, 0, 0))
-
- hitList= [[4, "+", 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)
- self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, doWeight=True))
- 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)
- self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, shift="auto"))
- 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]]
- 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]]
- 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)
- self.assertEquals(result, commoncode.findPeak(hitList, 0, 10, leftPlus=True, shift=3, returnShift=True))
+ result = commoncode.findPeak(hitList, 0, 0)
+ self.assertEquals([], result.topPos)
+ self.assertEquals(0.0, result.numHits)
+ self.assertEquals(array("f"), result.smoothArray)
+ self.assertEquals(0.0, result.numPlus)
+
+ hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
+ result = commoncode.findPeak(hitList, 0, 10)
+ self.assertEquals([6, 7], result.topPos)
+ self.assertEquals(1.0, result.numHits)
+ self.assertEquals(array("f", [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(1.0, result.numPlus)
+
+ result = commoncode.findPeak(hitList, 0, 10, doWeight=True)
+ self.assertEquals([6, 7], result.topPos)
+ self.assertEquals(0.5, result.numHits)
+ self.assertEquals(array('f', [0.0, 0.0, 0.0555555559694767, 0.1666666716337204, 0.3333333432674408, 0.4444444477558136, 0.5, 0.5, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(0.5, result.numPlus)
+
+ result = commoncode.findPeak(hitList, 0, 10, shift="auto")
+ self.assertEquals([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], result.topPos)
+ self.assertEquals(0.0, result.numHits)
+ self.assertEquals(array("f", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(0.0, result.numPlus)
+
+ result = commoncode.findPeak(hitList, 0, 10, shift="auto")
+ self.assertEquals([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], result.topPos)
+ self.assertEquals(0.0, result.numHits)
+ self.assertEquals(array("f", [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(0.0, result.numPlus)
+ self.assertEquals(6, result.shift)
+
+ hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
+ result = commoncode.findPeak(hitList, 0, 10, shift=3)
+ self.assertEquals([7], result.topPos)
+ self.assertEquals(1.0, result.numHits)
+ self.assertEquals(array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(1.0, result.numPlus)
+ self.assertEquals(3, result.shift)
+
+ hitList= [{"start": 4, "sense": "+", "weight": 0.5}]
+ result = commoncode.findPeak(hitList, 0, 10, leftPlus=True)
+ self.assertEquals([6, 7], result.topPos)
+ self.assertEquals(1.0, result.numHits)
+ self.assertEquals(array('f', [0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.8888888955116272, 1.0, 1.0, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(1.0, result.numPlus)
+ self.assertEquals(1.0, result.numLeftPlus)
+
+ result = commoncode.findPeak(hitList, 0, 10, leftPlus=True, shift=3)
+ self.assertEquals([7], result.topPos)
+ self.assertEquals(1.0, result.numHits)
+ self.assertEquals(array('f', [0.0, 0.0, 0.0, 0.0, 0.0, 0.1111111119389534, 0.3333333432674408, 0.66666668653488159, 0.0, 0.0]), result.smoothArray)
+ self.assertEquals(1.0, result.numPlus)
+ self.assertEquals(1.0, result.numLeftPlus)
+ self.assertEquals(3, result.shift)
#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"),
}
self.assertEquals(result, complementDict)
- regionDict = {"I": [("new feature", 100, 150, 50)]}
+ additionalRegion = Region.Region(100, 150)
+ additionalRegion.label = "new feature"
+ regionDict = {"I": [additionalRegion]}
featureDict = commoncode.getFeaturesByChromDict(self.genome, additionalRegionsDict=regionDict)
result = (100, 150, "new feature", "+", "custom")
self.assertEquals(result, featureDict["I"][0])
+
def testGetLocusByChromDict(self):
self.assertTrue(chrom in self.celegansChroms)
self.assertEquals(firstLoci[chrom], locusDict[chrom][0])
- regionDict = {"I": [("new region", 100, 150, 50)]}
+ additionalRegion = Region.Region(100, 150)
+ additionalRegion.label = "new region"
+ regionDict = {"I": [additionalRegion]}
locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict)
self.assertEquals((100, 150, "new region", 50), locusDict["I"][0])
locusDict = commoncode.getLocusByChromDict(self.genome, additionalRegionsDict=regionDict, keepSense=True)
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))
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})
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})
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})
projects / erange.git / blobdiff