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()
# fast.seqs2array_for_matmodel expects seqtype to be bytes
#self.seqtype = str.encode(self.seqtype) -> type bytes
#print(self.seqtype)
#self.seqtype = str.encode(self.seqtype)
#self.seqtype = str(self.seqtype).encode()
#print('In Models...')
#print(type(self.seqtype))
# if not bytes, change to bytes
if not (isinstance(self.seqtype,bytes)):
self.seqtype = str(self.seqtype).encode('utf-8')
#print(type(self.seqtype))
#print(type(self.seqtype))
#print(qc.seqtypes)
#seqs_to_use = list(map(bytes, str(seqs_to_use).encode('UTF-8')))
#seqs_to_use = list(map(bytes, seqs_to_use))
#print(seqs_to_use)
#if (isinstance(seqs_to_use[0], bytes)):
#print(seqs_to_use[0].decode())
# for i in range(len(seqs_to_use)):
# seqs_to_use[i] = seqs_to_use[i].decode()
# change elements to bytes if they're not bytes
if not (isinstance(seqs_to_use[0],bytes)):
#print('changing seq to bytes...')
for i in range(len(seqs_to_use)):
seqs_to_use[i] = str(seqs_to_use[i]).encode('utf-8')
#print('calling cython:')
#seqarray = fast.seqs2array_for_matmodel(list(seqs_to_use),self.seqtype)
seqarray = fast.seqs2array_for_matmodel(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
def dataset2mutarray_withwtseq(dataset_df, modeltype, wtseq, chunksize=1000):
# Determine the type of model and set seq2array function appropriately
if modeltype == 'MAT':
seqs2array = fast.seqs2array_for_matmodel
elif modeltype == 'NBR':
seqs2array = fast.seqs2array_for_nbrmodel
else:
raise SortSeqError('Unknown model type: %s' % modeltype)
# Determine seqtype, etc.
seqcol = qc.get_cols_from_df(dataset_df, 'seqs')[0]
seqtype = qc.colname_to_seqtype_dict[seqcol]
wtcol = qc.seqtype_to_wtcolname_dict[seqtype]
# Compute the wt sequence
wtrow = seqs2array([wtseq], seq_type=seqtype).ravel().astype(bool)
numfeatures = len(wtrow)
# Process dataframe in chunks
startrow = 0
endrow = startrow + chunksize - 1
numrows = dataset_df.shape[0]
# Fill in mutarray (a lil matrix) chunk by chunk
mutarray_lil = lil_matrix((numrows, numfeatures), dtype=int)
matrix_filled = False
while not matrix_filled:
if startrow >= numrows:
matrix_filled = True
continue
elif endrow >= numrows:
endrow = numrows - 1
matrix_filled = True
# Compute seqarray
seqlist = list(dataset_df[seqcol][startrow:(endrow + 1)])
seqarray = seqs2array(seqlist, seq_type=seqtype)
# Remove wt entries
tmp = seqarray.copy()
tmp[:, wtrow] = 0
# Store results from this chunk
mutarray_lil[startrow:(endrow + 1), :] = tmp
# Increment rows
startrow = endrow + 1
endrow = startrow + chunksize - 1
# Convert to csr matrix
mutarray_csr = mutarray_lil.tocsr()
# Return vararray as well as binary representation of wt seq
return mutarray_csr, wtrow
def main(filelist_df, tags_df=None, indir='./', seq_type=None):
""" Merges datasets listed in the filelist_df dataframe
"""
# Validate filelist
qc.validate_filelist(filelist_df)
# Read datasets into dictionary indexed by bin number
dataset_df_dict = {}
for item in filelist_df.iterrows():
# Autodetect fasta, fastq, or text file based on file extension
fn = indir + item[1]['file']
b = item[1]['bin']
if re.search(fasta_filename_patterns, fn):
df = io.load_dataset(fn, file_type='fasta', seq_type=seq_type)
elif re.search(fastq_filename_patterns, fn):
df = io.load_dataset(fn, file_type='fastq', seq_type=seq_type)
else:
df = io.load_dataset(fn, file_type='text', seq_type=seq_type)
dataset_df_dict[b] = df
# Merge datasets into one
out_df = merge_datasets(dataset_df_dict)
# Add seqs if given tags_df
if not tags_df is None:
qc.validate_tagkey(tags_df)
tag_col = 'tag'
# Test to make sure all tags in dataset are a subset of tags
data_tags = set(out_df[tag_col])
all_tags = set(tags_df[tag_col])
if not (data_tags <= all_tags):
sys.stderr.write('Some tags probably could not be identified.')
# Get name of seq column
seq_cols = qc.get_cols_from_df(tags_df, 'seqs')
if not len(seq_cols) == 1:
raise SortSeqError('Multiple seq columns; exaclty 1 required.')
seq_col = seq_cols[0]
# Set tag to be index column of dataframe
tags_df = tags_df.set_index(tag_col)
# Add seqs corresponding to each tag
tags = out_df[tag_col]
seqs = tags_df[seq_col][tags].values
if not all([type(x) == str for x in seqs]):
raise SortSeqError('Some looked-up seqs are not strings.')
out_df[seq_col] = tags_df[seq_col][tags].values
qc.validate_dataset(out_df)
return out_df
def dataset2seqarray(dataset_df, modeltype):
# Determine the type of model and set seq2array function appropriately
if modeltype == 'MAT':
seqs2array = fast.seqs2array_for_matmodel
elif modeltype == 'NBR':
seqs2array = fast.seqs2array_for_nbrmodel
else:
raise SortSeqError('Unknown model type: %s' % modeltype)
seqcol = qc.get_cols_from_df(dataset_df, 'seqs')[0]
seqtype = qc.colname_to_seqtype_dict[seqcol]
seqlist = list(dataset_df[seqcol])
seqarray = seqs2array(seqlist, seq_type=seqtype)
return seqarray
def __init__(self,model_df):
"""
Constructor takes model parameters in the form of a model dataframe
"""
model_df = qc.validate_model(model_df.copy(),fix=True)
seqtype, modeltype = qc.get_model_type(model_df)
if not modeltype=='MAT':
raise SortSeqError('Invalid modeltype: %s'%modeltype)
seq_dict,inv_dict = utils.choose_dict(seqtype,modeltype=modeltype)
self.seqtype = seqtype
self.seq_dict = seq_dict
self.inv_dict = inv_dict
self.df = model_df
self.length = model_df.shape[0]
# Extract matrix part of model dataframe
headers = qc.get_cols_from_df(model_df,'vals')
self.matrix = np.transpose(np.array(model_df[headers]))
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()
# python 3 fast.c update for string to bytes conversion
# if not bytes, change to bytes
if not (isinstance(self.seqtype,bytes)):
self.seqtype = str(self.seqtype).encode('utf-8')
# change elements to bytes if they're not bytes
if not (isinstance(seqs_to_use[0],bytes)):
#print('changing seq to bytes...')
for i in range(len(seqs_to_use)):
seqs_to_use[i] = str(seqs_to_use[i]).encode('utf-8')
seqarray = fast.seqs2array_for_nbrmodel(seqs_to_use,self.seqtype)
t1 = time.time()
# Compute and return values
vals = self.evaluate_on_seqarray(seqarray)
t2 = time.time()
return vals
def __init__(self,
data_df,
model_df,
start=0,
end=None,
err=False,
coarse_graining_level=0,
rsquared=False,
return_freg=False):
self.data_df = data_df
self.model_df = model_df
self.start = start
self.end = end
self.err = err
self.coarse_graining_level = coarse_graining_level
self.out_MI = None
self.out_std = None
self._input_checks()
dicttype, modeltype = qc.get_model_type(self.model_df)
seq_cols = qc.get_cols_from_df(self.data_df, 'seqs')
if not len(seq_cols) == 1:
raise SortSeqError('Dataframe has multiple seq cols: %s' %
str(seq_cols))
seq_dict, inv_dict = utils.choose_dict(dicttype, modeltype=modeltype)
# set name of sequences column based on type of sequence
type_name_dict = {'dna': 'seq', 'rna': 'seq_rna', 'protein': 'seq_pro'}
seq_col_name = type_name_dict[dicttype]
# Cut the sequences based on start and end, and then check if it makes sense
if (self.start != 0 or self.end):
self.data_df.loc[:,
seq_col_name] = self.data_df.loc[:,
seq_col_name].str.slice(
self.start,
self.end)
if modeltype == 'MAT':
if len(self.data_df.loc[0, seq_col_name]) != len(
self.model_df.loc[:, 'pos']):
print('predictive info class: BP lengths: ',
len(self.data_df.loc[0, seq_col_name]), " ",
len(self.model_df.loc[:, 'pos']))
raise SortSeqError(
'model length does not match dataset length')
elif modeltype == 'NBR':
if len(self.data_df.loc[0, seq_col_name]) != len(
self.model_df.loc[:, 'pos']) + 1:
raise SortSeqError(
'model length does not match dataset length')
col_headers = utils.get_column_headers(self.data_df)
if 'ct' not in self.data_df.columns:
self.data_df['ct'] = data_df[col_headers].sum(axis=1)
self.data_df = self.data_df[self.data_df.ct != 0]
if not self.end:
seqL = len(self.data_df[seq_col_name][0]) - self.start
else:
seqL = self.end - self.start
self.data_df = self.data_df[self.data_df[seq_col_name].apply(len)
== (seqL)]
# make a numpy array out of the model data frame
model_df_headers = [
'val_' + str(inv_dict[i]) for i in range(len(seq_dict))
]
value = np.transpose(np.array(self.model_df[model_df_headers]))
# now we evaluate the expression of each sequence according to the model.
seq_mat, wtrow = numerics.dataset2mutarray(self.data_df.copy(),
modeltype)
temp_df = self.data_df.copy()
# AT: what is this line trying to do?
temp_df['val'] = numerics.eval_modelmatrix_on_mutarray(
np.array(self.model_df[model_df_headers]), seq_mat, wtrow)
temp_sorted = temp_df.sort_values(by='val')
temp_sorted.reset_index(inplace=True, drop=True)
# we must divide by the total number of counts in each bin for the MI calculator
# temp_sorted[col_headers] = temp_sorted[col_headers].div(temp_sorted['ct'],axis=0)
if return_freg:
#fig, ax = plt.subplots()
MI, freg = EstimateMutualInfoforMImax.alt4(
temp_sorted,
coarse_graining_level=coarse_graining_level,
return_freg=return_freg)
#plt.imshow(freg, interpolation='nearest', aspect='auto')
#plt.savefig(return_freg)
else:
MI = EstimateMutualInfoforMImax.alt4(
temp_sorted,
coarse_graining_level=coarse_graining_level,
return_freg=return_freg)
if not self.err:
Std = np.NaN
else:
data_df_for_sub = self.data_df.copy()
sub_MI = np.zeros(15)
for i in range(15):
sub_df = data_df_for_sub.sample(
int(len(data_df_for_sub.index) / 2))
sub_df.reset_index(inplace=True, drop=True)
sub_MI[i], sub_std = PredictiveInfo(sub_df,
model_df,
err=False)
Std = np.std(sub_MI) / np.sqrt(2)
if rsquared:
#return (1 - 2 ** (-2 * MI)), (1 - 2 ** (-2 * Std))
self.out_MI, self.out_std = (1 - 2**(-2 * MI)), (1 - 2**(-2 * Std))
else:
#return MI, Std
self.out_MI, self.out_std = MI, Std
def __init__(self,
df,
lm='ER',
modeltype='MAT',
LS_means_std=None,
db=None,
iteration=30000,
burnin=1000,
thin=10,
runnum=0,
initialize='LS',
start=0,
end=None,
foreground=1,
background=0,
alpha=0.0,
pseudocounts=1,
drop_library=False,
verbose=False,
tm=None):
# set attributes
self.df = df
self.lm = lm
self.modeltype = modeltype
self.LS_means_std = LS_means_std
self.db = db
self.iteration = iteration
self.burnin = burnin
self.thin = thin
self.runnum = runnum
self.initialize = initialize
self.start = start
self.end = end
self.foreground = foreground
self.background = background
self.alpha = alpha
self.pseudocounts = pseudocounts
self.drop_library = drop_library
self.verbose = verbose
self.tm = tm
# output df
self.output_df = None
# validate parameters
self._input_checks()
# Determine dictionary
seq_cols = qc.get_cols_from_df(df, 'seqs')
if not len(seq_cols) == 1:
raise SortSeqError('Dataframe has multiple seq cols: %s' %
str(seq_cols))
dicttype = qc.colname_to_seqtype_dict[seq_cols[0]]
seq_dict, inv_dict = utils.choose_dict(dicttype, modeltype=modeltype)
'''Check to make sure the chosen dictionary type correctly describes
the sequences. An issue with this test is that if you have DNA sequence
but choose a protein dictionary, you will still pass this test bc A,C,
G,T are also valid amino acids'''
# set name of sequences column based on type of sequence
type_name_dict = {'dna': 'seq', 'rna': 'seq_rna', 'protein': 'seq_pro'}
seq_col_name = type_name_dict[dicttype]
lin_seq_dict, lin_inv_dict = utils.choose_dict(dicttype,
modeltype='MAT')
# wtseq = utils.profile_counts(df.copy(),dicttype,return_wtseq=True,start=start,end=end)
# wt_seq_dict_list = [{inv_dict[np.mod(i+1+seq_dict[w],len(seq_dict))]:i for i in range(len(seq_dict)-1)} for w in wtseq]
par_seq_dict = {
v: k
for v, k in seq_dict.items() if k != (len(seq_dict) - 1)
}
# drop any rows with ct = 0
df = df[df.loc[:, 'ct'] != 0]
df.reset_index(drop=True, inplace=True)
# If there are sequences of different lengths, then print error but continue
if len(set(df[seq_col_name].apply(len))) > 1:
sys.stderr.write('Lengths of all sequences are not the same!')
# select target sequence region
df.loc[:, seq_col_name] = df.loc[:, seq_col_name].str.slice(start, end)
df = utils.collapse_further(df)
col_headers = utils.get_column_headers(df)
# make sure all counts are ints
df[col_headers] = df[col_headers].astype(int)
# create vector of column names
val_cols = ['val_' + inv_dict[i] for i in range(len(seq_dict))]
df.reset_index(inplace=True, drop=True)
# Drop any sequences with incorrect length
if not end:
'''is no value for end of sequence was supplied, assume first seq is
correct length'''
seqL = len(df[seq_col_name][0]) - start
else:
seqL = end - start
df = df[df[seq_col_name].apply(len) == (seqL)]
df.reset_index(inplace=True, drop=True)
# Do something different for each type of learning method (lm)
if lm == 'ER':
if modeltype == 'NBR':
emat = self.Markov(df,
dicttype,
foreground=foreground,
background=background,
pseudocounts=pseudocounts)
else:
emat = self.Berg_von_Hippel(df,
dicttype,
foreground=foreground,
background=background,
pseudocounts=pseudocounts)
if lm == 'PR':
emat = self.convex_opt(df, seq_dict, inv_dict, col_headers, tm=tm, \
dicttype=dicttype, modeltype=modeltype)
if lm == 'LS':
'''First check that is we don't have a penalty for ridge regression,
that we at least have all possible base values so that the analysis
will not fail'''
if LS_means_std: # If user supplied preset means and std for each bin
means_std_df = io.load_meanstd(LS_means_std)
# change bin number to 'ct_number' and then use as index
labels = list(means_std_df['bin'].apply(self.add_label))
std = means_std_df['std']
std.index = labels
# Change Weighting of each sequence by dividing counts by bin std
df[labels] = df[labels].div(std)
means = means_std_df['mean']
means.index = labels
else:
means = None
# drop all rows without counts
df['ct'] = df[col_headers].sum(axis=1)
df = df[df.ct != 0]
df.reset_index(inplace=True, drop=True)
''' For sort-seq experiments, bin_0 is library only and isn't the lowest
expression even though it is will be calculated as such if we proceed.
Therefore is drop_library is passed, drop this column from analysis.'''
if drop_library:
try:
df.drop('ct_0', inplace=True)
col_headers = utils.get_column_headers(df)
if len(col_headers) < 2:
raise SortSeqError(
'''After dropping library there are no longer enough
columns to run the analysis''')
except:
raise SortSeqError(
'''drop_library option was passed, but no ct_0
column exists''')
# parameterize sequences into 3xL vectors
print('init learn model: \n')
print(par_seq_dict)
print('dict: ', dicttype)
raveledmat, batch, sw = utils.genweightandmat(df,
par_seq_dict,
dicttype,
means=means,
modeltype=modeltype)
# Use ridge regression to find matrix.
emat = self.Compute_Least_Squares(raveledmat,
batch,
sw,
alpha=alpha)
if lm == 'IM':
seq_mat, wtrow = numerics.dataset2mutarray(df.copy(), modeltype)
# this is also an MCMC routine, do the same as above.
if initialize == 'rand':
if modeltype == 'MAT':
emat_0 = utils.RandEmat(len(df[seq_col_name][0]),
len(seq_dict))
elif modeltype == 'NBR':
emat_0 = utils.RandEmat(
len(df[seq_col_name][0]) - 1, len(seq_dict))
elif initialize == 'LS':
emat_cols = [
'val_' + inv_dict[i] for i in range(len(seq_dict))
]
emat_0_df = LearnModel(df.copy(),
lm='LS',
modeltype=modeltype,
alpha=alpha,
start=0,
end=None,
verbose=verbose).output_df
emat_0 = np.transpose(np.array(emat_0_df[emat_cols]))
# pymc doesn't take sparse mat
elif initialize == 'PR':
emat_cols = [
'val_' + inv_dict[i] for i in range(len(seq_dict))
]
emat_0_df = LearnModel(df.copy(),
lm='PR',
modeltype=modeltype,
start=0,
end=None).output_df
emat_0 = np.transpose(np.array(emat_0_df[emat_cols]))
emat = self.MaximizeMI_memsaver(seq_mat,
df.copy(),
emat_0,
wtrow,
db=db,
iteration=iteration,
burnin=burnin,
thin=thin,
runnum=runnum,
verbose=verbose)
# We have infered out matrix.
# now format the energy matrices to get them ready to output
if (lm == 'IM' or lm == 'memsaver'):
if modeltype == 'NBR':
try:
emat_typical = gauge.fix_neighbor(np.transpose(emat))
except:
sys.stderr.write('Gauge Fixing Failed')
emat_typical = np.transpose(emat)
elif modeltype == 'MAT':
try:
emat_typical = gauge.fix_matrix(np.transpose(emat))
except:
sys.stderr.write('Gauge Fixing Failed')
emat_typical = np.transpose(emat)
elif lm == 'ER':
'''the emat for this format is currently transposed compared to other formats
it is also already a data frame with columns [pos,val_...]'''
if modeltype == 'NBR':
emat_cols = [
'val_' + inv_dict[i] for i in range(len(seq_dict))
]
emat_typical = emat[emat_cols]
else:
emat_cols = [
'val_' + inv_dict[i] for i in range(len(seq_dict))
]
emat_typical = emat[emat_cols]
try:
emat_typical = (gauge.fix_matrix((np.array(emat_typical))))
except:
sys.stderr.write('Gauge Fixing Failed')
emat_typical = emat_typical
elif (lm == 'MK'):
'''The model is a first order markov model and its gauge does not need
to be changed.'''
elif lm == 'PR':
emat_typical = np.transpose(emat)
else: # must be Least squares
emat_typical = utils.emat_typical_parameterization(
emat, len(seq_dict))
if modeltype == 'NBR':
try:
emat_typical = gauge.fix_neighbor(
np.transpose(emat_typical))
except:
sys.stderr.write('Gauge Fixing Failed')
emat_typical = np.transpose(emat_typical)
elif modeltype == 'MAT':
try:
emat_typical = gauge.fix_matrix(np.transpose(emat_typical))
except:
sys.stderr.write('Gauge Fixing Failed')
emat_typical = np.transpose(emat_typical)
em = pd.DataFrame(emat_typical)
em.columns = val_cols
# add position column
if modeltype == 'NBR':
pos = pd.Series(range(start, start - 1 + len(df[seq_col_name][0])),
name='pos')
else:
pos = pd.Series(range(start, start + len(df[seq_col_name][0])),
name='pos')
output_df = pd.concat([pos, em], axis=1)
# Validate model and return
output_df = qc.validate_model(output_df, fix=True)
self.output_df = output_df
