def gen_testVector(self, bed, vec):
with open(bed) as md:
bed_obj = read_bed(md)
with open(vec) as dmv:
vector_dmv = array(read_vector(dmv), "int8")
self.vec_obj = bed2vector(bed_obj, self.len_obj)
print "\nestimate\t", vector_dmv
print "result\t\t", self.vec_obj
self.assertTrue(alltrue(self.vec_obj == vector_dmv))
def _get_vector(self, bp):
bed = read_bed(bp)
divide_bed(bed, self.bin_size)
merge_bed(bed)
try:
vector = bed2vector(bed, self.chromosome_len)
except:
print bp
raise
return vector
def init_dhs_extraction(self):
with open(self.dhs_path) as dp:
dhs = read_bed(dp)
divide_bed(dhs, self.bin_size)
merge_bed(dhs)
self.dhs_vector = bed2vector(dhs, self.chromosome_len)
coverage = len(nonzero(self.dhs_vector)[0])
print coverage,"coverage"
ret = empty((coverage, len(self.beds_path)), dtype="int8")
current_col = 0
for bed_path in self.beds_path:
with open(bed_path) as bp:
ret[:,current_col] = self._bed2extracted_vector(bp)
current_col += 1
self.sparse = csr_matrix(ret,dtype="int16")
print "init DHS extraction finished"
def testMerge2(self):
divide_bed(self.bed_obj, 100)
merge_bed(self.bed_obj)
with open("./utest/test1_divided_merged.bed") as dmd:
self.bed_dmer = read_bed(dmd)
self.assertEqual(self.bed_obj, self.bed_dmer)
def testMerge(self):
merge_bed(self.bed_obj)
with open("./utest/test1_merged.bed") as md:
self.bed_mer = read_bed(md)
self.assertEqual(self.bed_obj, self.bed_mer)
def testDivide(self):
divide_bed(self.bed_obj, 100)
with open("./utest/test1_divided.bed") as dd:
self.bed_div = read_bed(dd)
self.assertEqual(self.bed_div, self.bed_obj)
def setUp(self):
with open("./utest/test1.bed") as tb:
self.bed_obj = read_bed(tb)
self.maxDiff = None