def downsample_elution(elution, downsample, seed=0):
"""
Return a new elution with every downsample-th fraction.
"""
down_elut = Struct()
down_elut.__dict__ = elution.__dict__.copy()
down_elut.mat = elution.mat[:,seed::2]
down_elut.fractions = elution.fractions[::2]
down_elut.name = elution.name + '_down%i' % downsample
return(down_elut)
def downsample_elution(elution, downsample, seed=0):
"""
Return a new elution with every downsample-th fraction.
"""
down_elut = Struct()
down_elut.__dict__ = elution.__dict__.copy()
down_elut.mat = elution.mat[:, seed::2]
down_elut.fractions = elution.fractions[::2]
down_elut.name = elution.name + "_down%i" % downsample
return down_elut
def subset_elution(elution, prot_set):
"""
Return an elution only containing the proteins contained in the
provided prot_set.
"""
newel = Struct()
newel.__dict__ = elution.__dict__.copy()
prot_inds, newprots = zip(*[(i, p) for i, p in enumerate(elution.prots) if p in prot_set])
newel.mat = elution.mat[prot_inds, :]
newel.prots = newprots
print len(newel.prots), "prots from", elution.filename, "in set"
return newel
def subset_elution(elution, prot_set):
"""
Return an elution only containing the proteins contained in the
provided prot_set.
"""
newel = Struct()
newel.__dict__ = elution.__dict__.copy()
prot_inds, newprots = zip(*[(i,p) for i,p in enumerate(elution.prots)
if p in prot_set])
newel.mat = elution.mat[prot_inds,:]
newel.prots = newprots
print len(newel.prots), 'prots from', elution.filename, 'in set'
return newel
def split_muliple_elutions(big_elut):
"""
Split an elution into multiple based on use of _fraction_elutions.
"""
elution_columns = _fraction_elutions(big_elut.fractions)
eluts = {}
for elution_name in elution_columns:
new_elut = Struct()
new_elut.__dict__ = big_elut.__dict__.copy()
new_elut.mat = big_elut.mat[:,elution_columns[elution_name]]
new_elut.fractions = list(np.array(big_elut.fractions)[elution_columns[elution_name]])
new_elut.filename = big_elut.filename + '__' + elution_name
eluts[elution_name] = new_elut
return eluts
def split_muliple_elutions(big_elut):
"""
Split an elution into multiple based on use of _fraction_elutions.
"""
elution_columns = _fraction_elutions(big_elut.fractions)
eluts = {}
for elution_name in elution_columns:
new_elut = Struct()
new_elut.__dict__ = big_elut.__dict__.copy()
new_elut.mat = big_elut.mat[:, elution_columns[elution_name]]
new_elut.fractions = list(np.array(big_elut.fractions)[elution_columns[elution_name]])
new_elut.filename = big_elut.filename + "__" + elution_name
eluts[elution_name] = new_elut
return eluts
def struct_copy(s):
print "Warning: this may not actually copy group variables."
newstruct = Struct()
newstruct.__dict__ = s.__dict__.copy()
return newstruct
def struct_copy(s):
print "Warning: this may not actually copy group variables."
newstruct = Struct()
newstruct.__dict__ = s.__dict__.copy()
return newstruct
def struct_copy(s):
newstruct = Struct()
newstruct.__dict__ = s.__dict__.copy()
return newstruct
