def IUAfreq(Loc, L):
patlist = {}
Loc.abbba = 0.
Loc.babba = 0.
Loc.abbaa = 0.
Loc.babaa = 0.
Loc.ababa = 0.
Loc.baaba = 0.
for col in Loc.seq.transpose():
patlist = fillin(L[0], 'p1', col, Loc.names, patlist)
patlist = fillin(L[1], 'p2', col, Loc.names, patlist)
patlist = fillin(L[2], 'p3a', col, Loc.names, patlist)
patlist = fillin(L[3], 'p3b', col, Loc.names, patlist)
patlist = fillin(L[4], 'o', col, Loc.names, patlist)
if not any([
all([i in ["N", '-'] for i in patlist['p1']]),
all([i in ["N", '-'] for i in patlist['p2']]),
all([i in ["N", '-'] for i in patlist['p3a']]),
all([i in ["N", '-'] for i in patlist['p3b']]),
all([i in ["N", '-'] for i in patlist['o']])
]):
if any([
i not in patlist['o']
for i in numpy.dstack((patlist['p3a'],
patlist['p3b']))[0][0]
]):
Loc = polyDstat5(Loc, patlist)
else:
None
else:
None
return Loc
def IUAfreq(Loc, L):
patlist = {}
Loc.abbba = 0.
Loc.babba = 0.
Loc.abbaa = 0.
Loc.babaa = 0.
Loc.ababa = 0.
Loc.baaba = 0.
for col in Loc.seq.transpose():
patlist = fillin(L[0], 'p1', col, Loc.names, patlist)
patlist = fillin(L[1], 'p2', col, Loc.names, patlist)
patlist = fillin(L[2], 'p3a', col, Loc.names, patlist)
patlist = fillin(L[3], 'p3b', col, Loc.names, patlist)
patlist = fillin(L[4], 'o', col, Loc.names, patlist)
if not any([ all([i in ["N",'-'] for i in patlist['p1']]),
all([i in ["N",'-'] for i in patlist['p2']]),
all([i in ["N",'-'] for i in patlist['p3a']]),
all([i in ["N",'-'] for i in patlist['p3b']]),
all([i in ["N",'-'] for i in patlist['o']]) ]):
if any([ i not in patlist['o'] for i in numpy.dstack((patlist['p3a'],patlist['p3b']))[0][0] ]):
Loc = polyDstat5(Loc, patlist)
else:
None
else:
None
return Loc
def IUAfreq(Loc, L):
patlist = {}
Loc.abbba = 0.
Loc.babba = 0.
Loc.abbaa = 0.
Loc.babaa = 0.
Loc.ababa = 0.
Loc.baaba = 0.
Loc.bbbaa = 0.
Loc.bbaba = 0.
Loc.aaaba = 0.
Loc.aabaa = 0.
Loc.abaaa = 0.
Loc.baaaa = 0.
for col in Loc.seq.transpose():
patlist = fillin(L[0], 'p1', col, Loc.names, patlist)
patlist = fillin(L[1], 'p2', col, Loc.names, patlist)
patlist = fillin(L[2], 'p3a', col, Loc.names, patlist)
patlist = fillin(L[3], 'p3b', col, Loc.names, patlist)
patlist = fillin(L[4], 'o', col, Loc.names, patlist)
" exclude sites with missing data "
if not any([ all([i in ["N",'-'] for i in patlist['p1']]),
all([i in ["N",'-'] for i in patlist['p2']]),
all([i in ["N",'-'] for i in patlist['p3a']]),
all([i in ["N",'-'] for i in patlist['p3b']]),
all([i in ["N",'-'] for i in patlist['o']]) ]):
" if site in not invariable "
isvar = len(set(col)-set(["N","-"])) > 1
if isvar:
" look for patterns in site "
Loc = polyDstatfoil(Loc, patlist)
return Loc
def IUAfreq(Loc, L):
patlist = {}
Loc.abbba = 0.
Loc.babba = 0.
Loc.abbaa = 0.
Loc.babaa = 0.
Loc.ababa = 0.
Loc.baaba = 0.
Loc.bbbaa = 0.
Loc.bbaba = 0.
Loc.aaaba = 0.
Loc.aabaa = 0.
Loc.abaaa = 0.
Loc.baaaa = 0.
for col in Loc.seq.transpose():
patlist = fillin(L[0], 'p1', col, Loc.names, patlist)
patlist = fillin(L[1], 'p2', col, Loc.names, patlist)
patlist = fillin(L[2], 'p3a', col, Loc.names, patlist)
patlist = fillin(L[3], 'p3b', col, Loc.names, patlist)
patlist = fillin(L[4], 'o', col, Loc.names, patlist)
" exclude sites with missing data "
if not any([
all([i in ["N", '-'] for i in patlist['p1']]),
all([i in ["N", '-'] for i in patlist['p2']]),
all([i in ["N", '-'] for i in patlist['p3a']]),
all([i in ["N", '-'] for i in patlist['p3b']]),
all([i in ["N", '-'] for i in patlist['o']])
]):
" if site in not invariable "
isvar = len(set(col) - set(["N", "-"])) > 1
if isvar:
" look for patterns in site "
Loc = polyDstatfoil(Loc, patlist)
return Loc