def evaluate(self,seqs):
# Check seqs container
if isinstance(seqs,pd.DataFrame):
seq_col = qc.get_cols_from_df(seqs,'seqs')[0]
seqs_to_use = list(seqs[seq_col])
elif not (isinstance(seqs,list) or isinstance(seqs,pd.Series)):
raise SortSeqError('Sequences must be input as a list, pd.Series, or pd.DataFrame')
else:
seqs_to_use = list(seqs)
# Check length
if len(seqs_to_use[0]) != self.length:
raise SortSeqError(\
'Energy Matrix Length does not equal Sequence Length')
# Compute seqmats
t0 = time.time()
seqarray = fast.seqs2array_for_matmodel(list(seqs_to_use),self.seqtype)
t1 = time.time()
# Compute and return values
vals = self.evaluate_on_seqarray(seqarray)
t2 = time.time()
#print 't1-t0 = %.4f, t1-t2 = %.4f'%(t1-t0,t2-t1)
return vals
sites = fast.seq2sitelist(seq, 20)
site_length = len(sites[0])
num_sites = len(sites)
t = time.time()
seq_dict, inv_dict = utils.choose_dict(seqtype, modeltype='MAT')
sitearray_p = np.zeros([num_sites, (site_length * len(seq_dict))], dtype=int)
for i, site in enumerate(sites):
sitearray_p[i, :] = utils.seq2mat(site, seq_dict).ravel()
p_time = time.time() - t
print 'python, seqs2array_for_matmodel: %f sec to convert %d %s seqs of length %d'%\
(p_time,num_sites,seqtype,site_length)
t = time.time()
sitearray = fast.seqs2array_for_matmodel(sites, seqtype, safe=False)
c_time = time.time() - t
print 'cython, seqs2array_for_matmodel: %f sec to convert %d %s seqs of length %d'%\
(c_time,num_sites,seqtype,site_length)
print '%.1f-fold speedup.' % (p_time / c_time)
print '-----------------------------'
# Test seqs2array_for_nbrmodel
sites = fast.seq2sitelist(seq, 20)
site_length = len(sites[0])
num_sites = len(sites)
t = time.time()
seq_dict, inv_dict = utils.choose_dict(seqtype, modeltype='NBR')
sites = fast.seq2sitelist(seq,20)
site_length = len(sites[0])
num_sites = len(sites)
t = time.time()
seq_dict,inv_dict = utils.choose_dict(seqtype,modeltype='MAT')
sitearray_p = np.zeros([num_sites,(site_length*len(seq_dict))],dtype=int)
for i, site in enumerate(sites):
sitearray_p[i,:] = utils.seq2mat(site,seq_dict).ravel()
p_time = time.time()-t
print 'python, seqs2array_for_matmodel: %f sec to convert %d %s seqs of length %d'%\
(p_time,num_sites,seqtype,site_length)
t = time.time()
sitearray = fast.seqs2array_for_matmodel(sites,seqtype,safe=False)
c_time = time.time()-t
print 'cython, seqs2array_for_matmodel: %f sec to convert %d %s seqs of length %d'%\
(c_time,num_sites,seqtype,site_length)
print '%.1f-fold speedup.'%(p_time/c_time)
print '-----------------------------'
# Test seqs2array_for_nbrmodel
sites = fast.seq2sitelist(seq,20)
site_length = len(sites[0])
num_sites = len(sites)
t = time.time()
seq_dict,inv_dict = utils.choose_dict(seqtype,modeltype='NBR')
