def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: a (response_headers, response_text) pair
"""
out = StringIO()
# heterozygous
print >> out, 'heterozygous region:'
a = fs.x
b = fs.y + fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
print >> out
# homozygous
print >> out, 'homozygous region:'
a = fs.x + fs.y
b = fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
print >> out
# misaligned
print >> out, 'misaligned homozygous region:'
a = fs.w + fs.x + fs.y
b = fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
return out.getvalue()
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: a (response_headers, response_text) pair
"""
out = StringIO()
# heterozygous
print >> out, 'heterozygous region:'
a = fs.x
b = fs.y + fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
print >> out
# homozygous
print >> out, 'homozygous region:'
a = fs.x + fs.y
b = fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
print >> out
# misaligned
print >> out, 'misaligned homozygous region:'
a = fs.w + fs.x + fs.y
b = fs.z
distn = DGRP.get_zygosity_distribution(a, b)
print >> out, distn_to_string(distn)
return out.getvalue()
def get_response_content(fs):
distn = DGRP.get_zygosity_distribution(fs.ref_length, fs.child_length)
out = StringIO()
print >> out, 'p(RR):', distn[0]
print >> out, 'p(RA):', distn[1]
print >> out, 'p(AA):', distn[2]
print >> out, 'p(AB):', distn[3]
return out.getvalue()
def __init__(self, dref, dchild, seqerr, nomcoverage, kmulticoverages):
"""
@param dref: a branch length parameter
@param dchild: a branch length parameter
@param seqerr: probability of sequence randomization
@param nomcoverage: nominal coverage
@param kmulticoverages: allowed multiples of nominal coverage
"""
mcov = GoodMultiCoverage(nomcoverage, kmulticoverages)
# define the states
r = seqerr
RR_states = [SinglePatternState(d, mcov) for d in gen_RR_distns(r)]
RA_states = [SinglePatternState(d, mcov) for d in gen_RA_distns(r)]
AA_states = [SinglePatternState(d, mcov) for d in gen_AA_distns(r)]
AB_states = [SinglePatternState(d, mcov) for d in gen_AB_distns(r)]
# define the distributions
RR = ReadCoverage.UniformMixture(RR_states)
RA = ReadCoverage.UniformMixture(RA_states)
AA = ReadCoverage.UniformMixture(AA_states)
AB = ReadCoverage.UniformMixture(AB_states)
states = (RR, RA, AA, AB)
zygo_distn = DGRP.get_zygosity_distribution(dref, dchild)
ReadCoverage.Mixture.__init__(self, states, zygo_distn)
