def __init__(self, pastafile, reffile, seqfile, verbose=False):
"""
Constructor
@param pastafile: filename for residue list
@type pastafile: string
@param reffile: filename for reference list (eg. BMRB ASCII file)
@type reffile: string
@param seqfile: filename for FASTA sequence file
@type seqfile: string
"""
fh = FileHandler()
## list of Residue.PastaResidue objects
self.residues = fh.read_pasta(pastafile, reffile)
## list of Residue.AminoAcid objects
self.amino_acids = fh.read_preset(reffile)
## list of Residue.AminoAcid objects
self.seq = fh.read_seq(seqfile, reffile)
self.P = None ## numpy.ndarray for typing posterior probabilities
self.L = None ## numpy.ndarray for linking constraints
self.S = None ## numpy.ndarray for aa type in sequence
self.A = None ## list of assignments and respective similarity score
## ILP STUFF
self.B = None ## list of assignments and respective costs
self.C = None ## cost matrix ILP
self.Xs = None ## assignment matrices from solution pool,
self.ILP_L = None ## Linking Matrix of ILP
self.typing_elapsed = 0
self.linking_elapsed = 0
self.mapping_elapsed = 0
self.full_running_time = 0
if __name__ == "__main__":
import pylab as pl
from numpy import max, mean, take, zeros
from Residue import PastaResidue, AminoAcid
from MaxLikelihood import Likelihood
from FileHandler import FileHandler
fh = FileHandler()
fn = "/is/ei/jhooge/EclipseWorkspaces/PASTA/PyPASTA/GMM/src/"\
"Classification/tests/reference_lists/bmrb.shift"
# pastalist = 'tests/residue_lists/all_singles.pasta'
pastalist = "Datasets/Ubiquitin/residue_lists/"\
"incompleteData/Ub_bmrb_missing_shifts_0.50.pasta"
statsfile = fn
amino_acids = fh.read_preset(fn)
residues = fh.read_pasta(pastalist, statsfile)
toAA = AbstractMapping.create("on_amino_acid")
toRes = AbstractMapping.create("on_residue")
aas = amino_acids
del aas[1]
L = Likelihood()
A = L.calc_likelihoods(residues, amino_acids, previous=False)
pl.matshow(A)
pl.colorbar()
pl.show()
i += 1
return x
if __name__ == '__main__':
from FileHandler import FileHandler
from numpy import argmax, mean, max
import pylab as pl
fh = FileHandler()
L = Likelihood()
# pastafile = 'multiple_test_files/Ubiquitin/Ub_new.pasta'
pastafile = 'tests/residue_lists/all_singles.pasta'
statsfile = 'shiftPresets/bmrb.shift'
residues = fh.read_pasta(pastafile, statsfile)
amino_acids = fh.read_preset(statsfile)
print ' '.join([aa.three_let for aa in amino_acids])
# r = residues[1]
# print r.name
# p11 = L.calc_likelihoods(residues, amino_acids, previous=False, summarize=mean)
# p12 = L.calc_likelihoods(residues, amino_acids, previous=True, summarize=mean)
p21 = L.calc_likelihoods(residues, amino_acids, previous=False, summarize=max)
p22 = L.calc_likelihoods(residues, amino_acids, previous=True, summarize=max)
print p21
print p22
# pl.matshow(p11)
# pl.colorbar()
# pl.matshow(p21)
