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 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 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