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("data/sample.bed", "BED") A = uBasicExp() A.load_with_parser(bedParser, 0) A.write_with_writer(writer) C = uBasicExp() bedParser = uParser("data/sample.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("data/sample.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("data/sample.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()
if (filename!=""): self.obj = self.libNGS.new_Writer(filename,typename) else: self.obj = self.libNGS.new_cout_Writer(typename) def __del__(self): self.libNGS.delete_Writer(self.obj) def write_token(self,token): self.libNGS.writeToken_writer(self.obj,token.obj) def write_string(self, text): self.libNGS.printString_Writer(self.obj,text) if __name__=="__main__": from uParser_wrapper import uParser samParser = uParser("data/sample.sam","SAM") bed6writer = uWriter("","BED6") someToken = uToken() print "Get first entry and write to standard output in bed6 to current.txt" someToken = samParser.get_next_entry() bed6writer.write_token(someToken) bed6writer = uWriter("current.txt","BED6") bed6writer.write_token(samParser.get_next_entry())
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 returnChromTests(): bedParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.bed","BED") A = uBasicExp() A.load_with_parser(bedParser,5) achrom= get_subset
else: self.obj = self.libNGS.new_cout_Writer(typename) def __del__(self): self.libNGS.delete_Writer(self.obj) def write_token(self,token): self.libNGS.writeToken_writer(self.obj,token.obj) def write_string(self, text): self.libNGS.printString_Writer(self.obj,text) if __name__=="__main__": from uParser_wrapper import uParser print "Loading a file, manually adjust to a local BAM file or will fail " bamParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BAM/H2AZ.bam","BAM") bed6writer = uWriter("","BED6") someToken = uToken() print "Get first entry and write to standard output in bed6" someToken = bamParser.get_next_entry() bed6writer.write_token(someToken) bed6writer = uWriter("current.txt","BED6") bed6writer =bamParser.get_next_entry() #while (A.eof()==0): # C.write_token(A.get_next_entry())
def firstTests(): from uBasicNGS_wrapper import uBasic from uParser_wrapper import uParser from uWriter_Wrapper import uWriter bedParser = uParser("data/sample.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("data/sample.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("data/sample.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 returnChromTests(): #not finished bedParser = uParser("data/sample.bed", "BED") A = uBasicExp() A.load_with_parser(bedParser, 5)