else:
print "invalid character found in secondary structure of " + secondary_structure.name
print "checked", i, "entries"
prot_trn = prot[0::2] # even-numbered indices
prot_tst = prot[1::2] # odd-numbered indices
sstr_trn = sstr[0::2] # even-numbered indices
sstr_tst = sstr[1::2] # odd-numbered indices
print len(prot_trn[0])
W = 5
print prot_trn[0]
print slidewin(prot_trn[0], W)
print len(slidewin(prot_trn[0], W))
nb = NaiveBayes([Protein_Alphabet for _ in range(W)], DSSP3_Alphabet)
# iterate over the sequence of proteins in the training set
# for i in range(len(prot_trn)):
print "-------------------------------------------------------"
for i in range(1):
subseqs = slidewin(prot_trn[i], W) # construct sub-seqs
subtarg = sstr_trn[i][W / 2:-W / 2 + 1] # secondary structure elem. remove the overhang
print subtarg
print sstr_trn[i]
# print subseqs, subtarg
for j in range(len(subseqs)):
nb.observe(subseqs[j], subtarg[j]) # let NB count
sstr = readFastaFile('sstr3.fa', DSSP3_Alphabet)
prot_trn = prot[0::2] # even-numbered indices
prot_tst = prot[1::2] # odd-numbered indices
sstr_trn = sstr[0::2] # even-numbered indices
sstr_tst = sstr[1::2] # odd-numbered indices
print "W, Q3, C, E, H"
for W in range(3, 50):
nb = NaiveBayes([Protein_Alphabet for _ in range(W)], DSSP3_Alphabet)
# iterate over the sequence of proteins in the training set
# for i in range(len(prot_trn)):
for i in range(len(prot_trn)):
subseqs = slidewin(prot_trn[i], W) # construct sub-seqs
subtarg = sstr_trn[i][W / 2:-W / 2 + 1] # secondary structure elem. remove the overhang
for j in range(len(subseqs)):
nb.observe(subseqs[j], subtarg[j]) # let NB count
# print "observing", subseqs[j], subtarg[j]
# create an array of zeroes of length of the secondary structure alphabet
cm = numpy.zeros((len(DSSP3_Alphabet), len(DSSP3_Alphabet)))
# iterate over the proteins in the test set
for i in range(len(prot_tst)):
subseqs = slidewin(prot_tst[i], W)
subtarg = sstr_tst[i][W / 2:-W / 2 + 1]
for j in range(len(subseqs)):
out = nb[subseqs[j]]
c_targ = DSSP3_Alphabet.index(subtarg[j])
"""
Created on 20/08/2014
@author: jacekrad
"""
from sequence import *
from prob import *
from __builtin__ import exit
from sys import stderr
from spred import slidewin
prot = readFastaFile("prot2.fa", Protein_Alphabet)
sstr = readFastaFile("sstr3.fa", DSSP3_Alphabet)
prot_trn = prot[0::2] # even-numbered indices
prot_tst = prot[1::2] # odd-numbered indices
sstr_trn = sstr[0::2] # even-numbered indices
sstr_tst = sstr[1::2] # odd-numbered indices
W = 5
print "Sequence length :", len(prot_trn[0])
print "Number of windows:", len(slidewin(prot_trn[0], W))
