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()
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 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")
