def secondTests():
writer= uWriter("","BEDGRAPH")
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
A.write_with_writer(writer)
C = uBasicExp()
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
C.load_with_parser(bedParser,0)
C.removeChr("chr2")
C.write_with_writer
print "before anything"
A.write_with_writer(writer)
L=A.get_overlapping_from_exp(C)
print "after get overlapping exp"
L.write_with_writer(writer)
L=A.get_overlapping_from_region("chr20",257180,257480)
print "after get overlapping region"
L.write_with_writer(writer)
#Need to test
#get_overlapping_from_chrom(self,chrom):
print "reset"
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
A.write_with_writer(writer)
print "after removeDistinct"
A.sort_sites()
A.remove_distinct("chr20",250000, 257700)
A.write_with_writer(writer)
print "reset"
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
print "after getDistinct"
A.sort_sites()
F=A.get_distinct("chr20",250000, 257700)
print F.count()
F.write_with_writer(writer)
print "ChrCount", F.get_chr_count()
print "Get subset no chrom"
print A.get_subset_count("chr22",250000, 257700)
deleteA= uBasic()
def secondTests():
writer= uWriter("","BEDGRAPH")
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
A.write_with_writer(writer)
C = uBasicExp()
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
C.load_with_parser(bedParser,0)
C.removeChr("chr2")
C.write_with_writer
print "before anything"
A.write_with_writer(writer)
L=A.get_overlapping_from_exp(C)
print "after get overlapping exp"
L.write_with_writer(writer)
L=A.get_overlapping_from_region("chr20",257180,257480)
print "after get overlapping region"
L.write_with_writer(writer)
#Need to test
#get_overlapping_from_chrom(self,chrom):
print "reset"
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
A.write_with_writer(writer)
print "after removeDistinct"
A.sort_sites()
A.remove_distinct("chr20",250000, 257700)
A.write_with_writer(writer)
print "reset"
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
A = uBasicExp()
A.load_with_parser(bedParser,0)
print "after getDistinct"
A.sort_sites()
F=A.get_distinct("chr20",250000, 257700)
print F.count()
F.write_with_writer(writer)
print "ChrCount", F.get_chr_count()
print "Get subset no chrom"
print A.get_subset_count("chr22",250000, 257700)
deleteA= uBasic()
def get_site(self,chr,pos): toReturn =uBasic() toReturn.obj= self.libNGS.getSite_basicExperiment(self.obj,chr,pos) return toReturn
def firstTests():
from uBasicNGS_wrapper import uBasic
from uParser_wrapper import uParser
from uWriter_Wrapper import uWriter
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
print "Make empty BasicExp"
A = uBasicExp()
B= uBasic("chr2",100,200)
print "Test is Chrom"
if (A.is_chrom("chr1")==0):
print "Chrom check ok"
else:
print A.is_chrom("chr1")
print "Test count"
print A.count()
print "Test add Data"
A.add_data_unit(B)
A.add_data_unit(uBasic("chr2",50,100))
print A.count()
if (A.is_chrom("chr2")==1):
print "Chrom check2 ok"
if (A.is_chrom("chr1")==1):
print "Chrom check fail"
print "before sort"
print A.is_sorted()
print "Test Sort"
A.sort_sites()
print "after sort"
print A.is_sorted()
print "Test Load With Parser"
A.load_with_parser(bedParser,5)
print A.count()
A.load_with_parser_path("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED",3)
print A.count()
writer= uWriter("","BEDGRAPH")
B= A.get_site("chr20",2)
print B.get_chr(),B.get_start(),B.get_end()
print A.count()
A.removeChr("chr20")
print A.count()
A.write_with_writer(writer)
A.sort_sites()
C = A.find_preceding_site("chr2",0)
print C
C = A.find_next_site("chr2",600)
print C
print "----"
A.remove_site("chr2",C)
A.write_with_writer(writer)
print "reloading"
A.load_with_parser_path("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED",0)
print "before subset"
A.sort_sites()
A.write_with_writer(writer)
#F = BasicExp()
A.remove_subset("chr2",30,120)
print "after subset"
A.write_with_writer(writer)
print "before setSize"
print A.get_chr_size("chr2")
print "after setSize"
A.set_chr_size("chr2",22999)
print A.get_chr_size("chr2")
print "after infer"
A.infer_chr_size()
print A.get_chr_size("chr2")
def return_overlapping(self, toCompare): toReturn = uBasic() toReturn.obj = self.NGSlib.returnOverlapping(self.obj, toCompare.obj) return toReturn
def ubasic_tests():
# Tests with the uBasicNGS
print "**** Tests constructor basic"
b = uBasic()
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "**** Tests constructor chr"
b = uBasic("chr1")
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "**** Tests constructor start"
b = uBasic("chr1", 1000)
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "**** Tests constructor end"
b = uBasic("chr1", 1000, 1200)
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "**** Tests constructor strand"
b = uBasic("chr1", 1000, 1200, "-")
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "**** Tests constructor score"
b = uBasic("chr1", 1000, 1200, "-", 2.4)
print "Chr: " + b.get_chr()
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Strand: " + str(b.get_strand())
print "Score: " + str(b.get_score())
print "**** Misc tests"
b = uBasic("chr1", 100, 200)
print b.get_chr()
b.set_chr("chr2")
print b.get_chr()
print b.get_strand()
b.set_strand("-")
print b.get_strand()
print "IsReverse: " + str(b.is_reverse())
print "**** Start/End/Length tests with set/get/extend/trim"
print "Base Values"
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "set_start(50), set_end(250)"
b.set_start(50)
b.set_end(250)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print"set_start_end(75,125)"
b.set_start_end(75,125)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "extend_site(10)"
b.extend_site(10)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "trim_site(30)"
b.trim_site(30)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "extend_site(10,20)"
b.extend_site(10,20)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "trim_site(5,10)"
b.trim_site(5,10)
print "Start: " + str(b.get_start())
print "End: " + str(b.get_end())
print "Length: " + str(b.get_length())
print "**** Score tests"
#print "Score: " + str(b.get_score())
print "ScoreCount: " + str(b.get_score_count())
print "set_score(100.2)"
b.set_score(100.3)
print "Score: " + str(b.get_score())
print "ScoreCount: " + str(b.get_score_count())
b.set_score(233.24, 1)
print "Score(0): " + str(b.get_score(0))
print "Score(1): " + str(b.get_score(1))
print "ScoreCount: " + str(b.get_score_count())
print "ScoreList: " + str(b.get_score_list())
print "**** Tests for does_overlap"
b2 = uBasic("chr2", 100, 200)
b3 = uBasic("chr2", 201, 300)
b4 = uBasic("chr1", 100, 200)
print "does overlap: " + str(b.does_overlap(b2))
print "does not overlap: " + str(b.does_overlap(b3))
print "does overlap not same chr: " + str(b.does_overlap(b4))
print "**** Tests for returnOverlapping"
c = b.return_overlapping(b2)
print "Overlap: chr: " + c.get_chr()
print "Overlap: start: " + str(c.get_start())
print "Overlap: end: " + str(c.get_end())
print "**** Tests for return_merge"
c = b.return_merge(b2)
print "Merge: chr: " + c.get_chr()
print "Merge: start: " + str(c.get_start())
print "Merge: end: " + str(c.get_end())
def ManyTests():
print "--------------------------"
print "TESTS: uBasicNGSChrom"
print "--------------------------"
print "**** Tests for constructor"
print "No param:"
chrom = uBasicChrom()
print "chr: " + chrom.get_chr()
print "chrSize: " + str(chrom.get_chrom_size())
print "Chrom Name"
chromName = uBasicChrom("chr5")
print "chr: " + chromName.get_chr()
print "chrSize: " + str(chromName.get_chrom_size())
print "Chrom Name Size:"
chromNameSize = uBasicChrom("chr3", 123456)
print "chr: " + chromNameSize.get_chr()
print "chrSize: " + str(chromNameSize.get_chrom_size())
print "Chrom Size:"
chrom_size = uBasicChrom(chromosomeSize=123456)
print "chr: " + chrom_size.get_chr()
print "chrSize: " + str(chrom_size.get_chrom_size())
print ""
print "**** Tests for get_copy"
chromCopy = chromNameSize.get_copy()
print "chr: " + chromCopy.get_chr()
print "chrSize: " + str(chromCopy.get_chrom_size())
print ""
print "**** Tests for add_data functions"
chromAddData = uBasicChrom("chr3")
basicAddData = uBasic("chr3", 100, 200)
chromAddData.add_data(basicAddData)
print "chr: " + chromAddData.get_chr()
print "chrSize: " + str(chromAddData.get_chrom_size())
print ""
print "**** Tests for infer_chr_size "
chromInfer = uBasicChrom("chr3")
chromInfer.add_data(uBasic("chr3", 1000, 3000))
print "chrSize (before): " + str(chromInfer.get_chrom_size())
chromInfer.infer_chr_size()
print "chrSize (after): " + str(chromInfer.get_chrom_size())
chromInfer = uBasicChrom()
print "chrSize (empty):" + str(chromInfer.get_chrom_size())
print ""
print "**** Tests for the divide_items_into_n_bins function"
chromDivide = uBasicChrom("chr4")
chromDivide.add_data(uBasic("chr4", 1000, 3000))
print "count (before): " + str(chromDivide.count())
chromDivide.divide_items_into_n_bins(10, "IGNORE")
print "count (after): " + str(chromDivide.count())
print ""
print "**** Tests for the divideItemsIntoBinofSize function"
chromDivide = uBasicChrom("chr4")
chromDivide.add_data(uBasic("chr4", 1000, 2000))
print "count (before): " + str(chromDivide.count())
chromDivide.divide_items_into_bin_of_size(20, "IGNORE")
print "count (after): " + str(chromDivide.count())
print ""
print "**** Tests for the function getSite"
chromGetSite = uBasicChrom("chr1")
chromGetSite.add_data(uBasic("chr1", 300, 500))
aSite = chromGetSite.get_site(0)
print "getSite: chr: " + aSite.get_chr()
print "getSite: start: " + str(aSite.get_start())
print "getSite: end: " + str(aSite.get_end())
print ""
print "**** Tests for the statistic functions"
chromStats = uBasicChrom("chrX")
chromStats.add_data(uBasic("chrX", 300, 500))
chromStats.add_data(uBasic("chrX", 300, 600))
chromStats.add_data(uBasic("chrX", 400, 500))
print "avg: " + str(chromStats.avg_site_size())
print "min: " + str(chromStats.min_site_size())
print "max: " + str(chromStats.max_site_size())
print "sum: " + str(chromStats.sum_site_size())
print "count: " + str(chromStats.count())
print "**** Tests for adding random sites"
chromAddRandom = uBasicChrom("chrY")
chromAddRandom.set_chr_size(100000)
chromAddRandom.add_random_sites(100, 10,10)
print "Count: " + str(chromAddRandom.count())
writer= uWriter("","BEDGRAPH")
chromAddRandom.write_with_writer(writer)
print ""
print "**** Tests for get_overlapping/get_overlapping_count (other Chrom)"
chromOverlap1 = uBasicChrom("chr1")
chromOverlap1.add_data(uBasic("chr1", 100, 200))
chromOverlap1.add_data(uBasic("chr1", 400, 800))
chromOverlap1.add_data(uBasic("chr1", 1000, 1200))
print "Different chrom:"
chromOverlap2 = uBasicChrom("chr2")
chromOverlap2.add_data(uBasic("chr2", 100, 200))
chromOverlap2.add_data(uBasic("chr2", 400, 800))
chromOverlap2.add_data(uBasic("chr2", 1000, 1200))
chromOverlapResult = chromOverlap1.get_overlapping(chromOverlap2)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromOverlap1.get_overlapping_count(chromOverlap2))
print "No overlap:"
chromOverlap3 = uBasicChrom("chr1")
chromOverlap3.add_data(uBasic("chr1", 1300, 1400))
chromOverlap3.add_data(uBasic("chr1", 1400, 1800))
chromOverlap3.add_data(uBasic("chr1", 11000, 11200))
chromOverlapResult = chromOverlap1.get_overlapping(chromOverlap3)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromOverlap1.get_overlapping_count(chromOverlap3))
print "Some overlap:"
chromOverlap4 = uBasicChrom("chr1")
chromOverlap4.add_data(uBasic("chr1", 100, 150))
chromOverlap4.add_data(uBasic("chr1", 400, 900))
chromOverlap4.add_data(uBasic("chr1", 11000, 11200))
chromOverlapResult = chromOverlap1.get_overlapping(chromOverlap4)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromOverlap1.get_overlapping_count(chromOverlap4))
print "All overlap: "
chromOverlap5 = uBasicChrom("chr1")
chromOverlap5.add_data(uBasic("chr1", 100, 200))
chromOverlap5.add_data(uBasic("chr1", 400, 800))
chromOverlap5.add_data(uBasic("chr1", 1000, 1200))
chromOverlapResult = chromOverlap1.get_overlapping(chromOverlap5)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromOverlap1.get_overlapping_count(chromOverlap5))
print ""
print "**** Tests for get_overlapping/get_overlapping_count (basic)"
chromBasicOverlap1 = uBasicChrom("chr2")
chromBasicOverlap1.add_data(uBasic("chr2", 100, 200))
chromBasicOverlap1.add_data(uBasic("chr2", 400, 800))
chromBasicOverlap1.add_data(uBasic("chr2", 1000, 1200))
print "chromBasicOverlap1.count(): " + str(chromBasicOverlap1.count())
basicOverlap = uBasic("chr2", 50, 900)
chromOverlapResult = chromBasicOverlap1.get_overlapping_basic(basicOverlap)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromBasicOverlap1.get_overlapping_count_basic(basicOverlap))
aSite = chromOverlapResult.get_site(0)
print "get_site: chr: " + aSite.get_chr()
print "get_site: start: " + str(aSite.get_start())
print "get_site: end: " + str(aSite.get_end())
print ""
print "**** Tests for get_overlapping/get_overlapping_count (region)"
chromRegionOverlap1 = uBasicChrom("chr3")
chromRegionOverlap1.add_data(uBasic("chr3", 100, 200))
chromRegionOverlap1.add_data(uBasic("chr3", 400, 800))
chromRegionOverlap1.add_data(uBasic("chr3", 1000, 1200))
chromOverlapResult = chromRegionOverlap1.get_overlapping_region(50, 900)
print "Result Count: " + str(chromOverlapResult.count())
print "get_overlapCount: " + str(chromBasicOverlap1.get_overlapping_count_region(50, 900))
print ""
print "**** Tests for get_not_overlapping (other Chrom)"
chromNotOverlap1 = uBasicChrom("chr1")
chromNotOverlap1.add_data(uBasic("chr1", 100, 200))
chromNotOverlap1.add_data(uBasic("chr1", 400, 800))
chromNotOverlap1.add_data(uBasic("chr1", 1000, 1200))
print "Different chrom:"
chromNotOverlap2 = uBasicChrom("chr2")
chromNotOverlap2.add_data(uBasic("chr2", 100, 200))
chromNotOverlap2.add_data(uBasic("chr2", 400, 800))
chromNotOverlap2.add_data(uBasic("chr2", 1000, 1200))
chromNotOverlapResult = chromNotOverlap1.get_not_overlapping(chromNotOverlap2)
print "Result Count: " + str(chromNotOverlapResult.count())
# print "get_not_overlapCount: " + str(chromNotOverlap1.get_not_overlapping_count(chromNotOverlap2))
print "No overlap:"
chromNotOverlap3 = uBasicChrom("chr1")
chromNotOverlap3.add_data(uBasic("chr1", 1300, 1400))
chromNotOverlap3.add_data(uBasic("chr1", 1400, 1800))
chromNotOverlap3.add_data(uBasic("chr1", 11000, 11200))
chromNotOverlapResult = chromNotOverlap1.get_not_overlapping(chromNotOverlap3)
print "Result Count: " + str(chromNotOverlapResult.count())
# print "get_not_overlapCount: " + str(chromNotOverlap1.get_not_overlapping_count(chromNotOverlap3))
print "Some overlap:"
chromNotOverlap4 = uBasicChrom("chr1")
chromNotOverlap4.add_data(uBasic("chr1", 100, 150))
chromNotOverlap4.add_data(uBasic("chr1", 400, 900))
chromNotOverlap4.add_data(uBasic("chr1", 11000, 11200))
chromNotOverlapResult = chromNotOverlap1.get_not_overlapping(chromNotOverlap4)
print "Result Count: " + str(chromNotOverlapResult.count())
# print "get_overlapCount: " + str(chromNotOverlap1.get_not_overlapping_count(chromNotOverlap4))
print "All overlap: "
chromNotOverlap5 = uBasicChrom("chr1")
chromNotOverlap5.add_data(uBasic("chr1", 100, 200))
chromNotOverlap5.add_data(uBasic("chr1", 400, 800))
chromNotOverlap5.add_data(uBasic("chr1", 1000, 1200))
chromNotOverlapResult = chromNotOverlap1.get_not_overlapping(chromNotOverlap5)
print "Result Count: " + str(chromNotOverlapResult.count())
def firstTests():
from uBasicNGS_wrapper import uBasic
from uParser_wrapper import uParser
from uWriter_Wrapper import uWriter
bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED")
print "Make empty BasicExp"
A = uBasicExp()
A.sort_sites()
B= uBasic("chr2",100,200)
print "Test is Chrom"
if (A.is_chrom("chr1")==0):
print "Chrom check ok"
else:
print A.is_chrom("chr1")
print "Test count"
print A.count()
print "Test add Data"
A.add_data_unit(B)
A.add_data_unit(uBasic("chr2",50,100))
print A.count()
if (A.is_chrom("chr2")==1):
print "Chrom check2 ok"
if (A.is_chrom("chr1")==1):
print "Chrom check fail"
print "before sort"
print A.is_sorted()
print "Test Sort"
A.sort_sites()
print "after sort"
print A.is_sorted()
print "Test Load With Parser"
A.load_with_parser(bedParser,5)
print A.count()
A.load_with_parser_path("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED",3)
print A.count()
writer= uWriter("","BEDGRAPH")
B= A.get_site("chr20",2)
print B.get_chr(),B.get_start(),B.get_end()
print A.count()
A.removeChr("chr20")
print A.count()
A.write_with_writer(writer)
A.sort_sites()
C = A.find_preceding_site("chr2",0)
print C
C = A.find_next_site("chr2",600)
print C
print "----"
A.remove_site("chr2",C)
A.write_with_writer(writer)
print "reloading"
A.load_with_parser_path("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED",0)
print "before subset"
A.sort_sites()
A.write_with_writer(writer)
#F = BasicExp()
A.remove_subset("chr2",30,120)
print "after subset"
A.write_with_writer(writer)
print "before setSize"
print A.get_chr_size("chr2")
print "after setSize"
A.set_chr_size("chr2",22999)
print A.get_chr_size("chr2")
print "after infer"
A.infer_chr_size()
print A.get_chr_size("chr2")
def get_site(self,chr,pos): toReturn =uBasic() toReturn.obj= self.libNGS.getSite_basicExperiment(self.obj,chr,pos) return toReturn
def get_site(self, position): toReturn = uBasic() toReturn.obj = self.lib.getSite(self.obj, position) return toReturn
def return_merge(self, toCompare): toReturn = uBasic() toReturn.obj = self.NGSlib.returnMerge(self.obj, toCompare.obj) return toReturn
