def read(self, input_handle):
"""Read patterns from the specified handle.
"""
all_patterns = []
while True:
cur_line = input_handle.readline()
if not (cur_line):
break
cur_pattern = cur_line.rstrip()
# split up signatures
if self.separator in cur_pattern:
cur_pattern = tuple(cur_pattern.split(self.separator))
if self._alphabet is not None:
# make single patterns (not signatures) into lists, so we
# can check signatures and single patterns the same
if not isinstance(cur_pattern, tuple):
test_pattern = [cur_pattern]
else:
test_pattern = cur_pattern
for pattern_item in test_pattern:
pattern_seq = Seq(pattern_item, self._alphabet)
if not (_verify_alphabet(pattern_seq)):
raise ValueError(
"Pattern %s not matching alphabet %s" %
(cur_pattern, self._alphabet))
all_patterns.append(cur_pattern)
return all_patterns
def read(self, input_handle):
"""Read patterns from the specified handle.
"""
all_patterns = []
while True:
cur_line = input_handle.readline()
if not(cur_line):
break
cur_pattern = cur_line.rstrip()
# split up signatures
if self.separator in cur_pattern:
cur_pattern = tuple(cur_pattern.split(self.separator))
if self._alphabet is not None:
# make single patterns (not signatures) into lists, so we
# can check signatures and single patterns the same
if not isinstance(cur_pattern, tuple):
test_pattern = [cur_pattern]
else:
test_pattern = cur_pattern
for pattern_item in test_pattern:
pattern_seq = Seq(pattern_item, self._alphabet)
if not(_verify_alphabet(pattern_seq)):
raise ValueError("Pattern %s not matching alphabet %s"
% (cur_pattern, self._alphabet))
all_patterns.append(cur_pattern)
return all_patterns
def _get_signature_dict(self, seq_records, sig_size, max_gap):
"""Return a dictionary with all signatures and their counts.
This internal function does all of the hard work for the
find_signatures function.
"""
if self._alphabet_strict:
alphabet = seq_records[0].seq.alphabet
else:
alphabet = None
# loop through all records to find signatures
all_sigs = {}
for seq_record in seq_records:
# if we are working with alphabets, make sure we are consistent
if alphabet is not None:
assert seq_record.seq.alphabet == alphabet, \
"Working with alphabet %s and got %s" % \
(alphabet, seq_record.seq.alphabet)
# now start finding signatures in the sequence
largest_sig_size = sig_size * 2 + max_gap
for start in range(len(seq_record.seq) - (largest_sig_size - 1)):
# find the first part of the signature
first_sig = str(seq_record.seq[start:start + sig_size])
# now find all of the second parts of the signature
for second in range(start + 1, (start + 1) + max_gap):
second_sig = str(seq_record.seq[second:second + sig_size])
# if we are being alphabet strict, make sure both parts
# of the sig fall within the specified alphabet
if alphabet is not None:
first_seq = Seq(first_sig, alphabet)
second_seq = Seq(second_sig, alphabet)
if _verify_alphabet(first_seq) \
and _verify_alphabet(second_seq):
all_sigs = self._add_sig(all_sigs,
(first_sig, second_sig))
# if we are not being strict, just add the motif
else:
all_sigs = self._add_sig(all_sigs,
(first_sig, second_sig))
return all_sigs
def _get_signature_dict(self, seq_records, sig_size, max_gap):
"""Return a dictionary with all signatures and their counts.
This internal function does all of the hard work for the
find_signatures function.
"""
if self._alphabet_strict:
alphabet = seq_records[0].seq.alphabet
else:
alphabet = None
# loop through all records to find signatures
all_sigs = {}
for seq_record in seq_records:
# if we are working with alphabets, make sure we are consistent
if alphabet is not None:
assert seq_record.seq.alphabet == alphabet, \
"Working with alphabet %s and got %s" % \
(alphabet, seq_record.seq.alphabet)
# now start finding signatures in the sequence
largest_sig_size = sig_size * 2 + max_gap
for start in range(len(seq_record.seq) - (largest_sig_size - 1)):
# find the first part of the signature
first_sig = str(seq_record.seq[start:start + sig_size])
# now find all of the second parts of the signature
for second in range(start + 1, (start + 1) + max_gap):
second_sig = str(seq_record.seq[second: second + sig_size])
# if we are being alphabet strict, make sure both parts
# of the sig fall within the specified alphabet
if alphabet is not None:
first_seq = Seq(first_sig, alphabet)
second_seq = Seq(second_sig, alphabet)
if _verify_alphabet(first_seq) \
and _verify_alphabet(second_seq):
all_sigs = self._add_sig(all_sigs,
(first_sig, second_sig))
# if we are not being strict, just add the motif
else:
all_sigs = self._add_sig(all_sigs,
(first_sig, second_sig))
return all_sigs
def _get_motif_dict(self, seq_records, motif_size):
"""Return a dictionary with information on motifs.
This internal function essentially does all of the hard work for
finding motifs, and returns a dictionary containing the found motifs
and their counts. This is internal so it can be reused by
find_motif_differences.
"""
if self.alphabet_strict:
alphabet = seq_records[0].seq.alphabet
else:
alphabet = None
# loop through all records to find the motifs in the sequences
all_motifs = {}
for seq_record in seq_records:
# if we are working with alphabets, make sure we are consistent
if alphabet is not None:
assert seq_record.seq.alphabet == alphabet, \
"Working with alphabet %s and got %s" % \
(alphabet, seq_record.seq.alphabet)
# now start finding motifs in the sequence
for start in range(len(seq_record.seq) - (motif_size - 1)):
motif = str(seq_record.seq[start:start + motif_size])
# if we are being alphabet strict, make sure the motif
# falls within the specified alphabet
if alphabet is not None:
motif_seq = Seq(motif, alphabet)
if _verify_alphabet(motif_seq):
all_motifs = self._add_motif(all_motifs, motif)
# if we are not being strict, just add the motif
else:
all_motifs = self._add_motif(all_motifs, motif)
return all_motifs
def _get_motif_dict(self, seq_records, motif_size):
"""Return a dictionary with information on motifs.
This internal function essentially does all of the hard work for
finding motifs, and returns a dictionary containing the found motifs
and their counts. This is internal so it can be reused by
find_motif_differences.
"""
if self.alphabet_strict:
alphabet = seq_records[0].seq.alphabet
else:
alphabet = None
# loop through all records to find the motifs in the sequences
all_motifs = {}
for seq_record in seq_records:
# if we are working with alphabets, make sure we are consistent
if alphabet is not None:
assert seq_record.seq.alphabet == alphabet, \
"Working with alphabet %s and got %s" % \
(alphabet, seq_record.seq.alphabet)
# now start finding motifs in the sequence
for start in range(len(seq_record.seq) - (motif_size - 1)):
motif = str(seq_record.seq[start:start + motif_size])
# if we are being alphabet strict, make sure the motif
# falls within the specified alphabet
if alphabet is not None:
motif_seq = Seq(motif, alphabet)
if _verify_alphabet(motif_seq):
all_motifs = self._add_motif(all_motifs, motif)
# if we are not being strict, just add the motif
else:
all_motifs = self._add_motif(all_motifs, motif)
return all_motifs