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#!/usr/bin/env python3
class A3MFormatError(Exception):
def __init__(self, value):
self.value = "ERROR: "+value
def __str__(self):
return repr(self.value)
class A3M_Container:
RESIDUES = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
VALID_MATCH_STATES = set(RESIDUES)
VALID_INSERTION_STATES = set(RESIDUES.lower())
VALID_GAP_STATES = set("-.")
VALID_SS_CONF_STATES = set("0123456789")
VALID_SS_STATES = set("ECH")
VALID_DSSP_STATES = set("CHBEGITS-")
def __init__(self):
self.header = None
self.annotations = dict()
self.consensus = None
self.sequences = []
self.nr_match_states = None
@property
def number_sequences(self):
"""get the current number of protein sequences"""
return len(self.sequences)
def check_and_add_sequence(self, header, sequence):
try:
if (not self.check_and_add_annotation(header, sequence) and
not self.check_and_add_consensus(header, sequence)):
self.check_sequence(sequence)
self.sequences.append((header, sequence))
except A3MFormatError as e:
raise e
def check_and_add_consensus(self, header, sequence):
header_name = header[1:].split()[0]
if header_name.endswith("_consensus"):
if self.consensus:
raise A3MFormatError("Multiple definitions of consensus!")
else:
self.check_sequence(sequence)
self.consensus = (header, sequence)
return True
else:
return False
def check_and_add_annotation(self, header, sequence):
annotation_classes = [
("ss_conf", self.check_ss_conf),
("ss_pred", self.check_ss_pred),
("ss_dssp", self.check_dssp)
]
for (annotation_name, check) in annotation_classes:
if(header[1:].startswith(annotation_name)):
if(annotation_name in self.annotations):
raise A3MFormatError(
"Multiple definitions of {}!".format(annotation_name)
)
elif check(sequence):
self.annotations[annotation_name] = sequence
return True
return False
def check_match_states(self, match_states):
if not self.nr_match_states:
self.nr_match_states = match_states
if match_states == 0:
raise A3MFormatError("Sequence with zero match states!")
elif match_states != self.nr_match_states:
raise A3MFormatError(
("Sequence with diverging number "
"of match states ({} vs. {})!").format(
match_states,
self.nr_match_states
)
)
def check_ss_conf(self, sequence):
count_match_states = sum((c in self.VALID_SS_CONF_STATES
or c in self.VALID_GAP_STATES)
for c in sequence)
self.check_match_states(count_match_states)
invalid_states = set(sequence) - self.VALID_SS_CONF_STATES
invalid_states -= self.VALID_GAP_STATES
if len(invalid_states):
raise A3MFormatError(
("Undefined character(s) '{}' in predicted "
"secondary structure confidence!").format(invalid_states))
else:
return True
def check_ss_pred(self, sequence):
count_match_states = sum((c in self.VALID_SS_STATES
or c in self.VALID_GAP_STATES)
for c in sequence)
self.check_match_states(count_match_states)
invalid_states = set(sequence) - self.VALID_SS_STATES
invalid_states -= self.VALID_GAP_STATES
if len(invalid_states):
raise A3MFormatError(
("Undefined character(s) '{}' in predicted "
"secondary structure!").format(invalid_states))
else:
return True
def check_dssp(self, sequence):
count_match_states = sum(
(c in self.VALID_DSSP_STATES) for c in sequence)
self.check_match_states(count_match_states)
invalid_states = set(sequence) - self.VALID_DSSP_STATES
if len(invalid_states):
raise A3MFormatError(
("Undefined character(s) '{}' in "
"dssp annotation!").format(invalid_states))
else:
return True
def check_sequence(self, sequence):
count_match_states = sum((c in self.VALID_MATCH_STATES
or c in self.VALID_GAP_STATES)
for c in sequence)
self.check_match_states(count_match_states)
invalid_states = set(sequence) - self.VALID_MATCH_STATES
invalid_states -= self.VALID_GAP_STATES
invalid_states -= self.VALID_INSERTION_STATES
if len(invalid_states):
raise A3MFormatError(
("Undefined character(s) '{}' in "
"protein sequence!").format(invalid_states))
else:
return True
def get_sub_sequence(self, sequence, limits):
sub_sequence = []
for (start, end) in limits:
start_pos = 0
pos = -1
for i in range(len(sequence)):
if (sequence[i] in self.VALID_MATCH_STATES or
sequence[i] in self.VALID_GAP_STATES):
pos += 1
if pos + 1 == start:
start_pos = i
break
end_pos = 0
pos = -1
for i in range(len(sequence)):
if (sequence[i] in self.VALID_MATCH_STATES or
sequence[i] in self.VALID_GAP_STATES):
pos += 1
if pos + 1 == end:
end_pos = i
break
sub_sequence.append(sequence[start_pos:end_pos+1])
return "".join(sub_sequence)
def __str__(self):
content = []
if self.header:
content.append(self.header)
if self.consensus:
content.append(self.consensus[0])
content.append(self.consensus[1])
for (header, sequence) in self.sequences:
content.append(header)
content.append(sequence)
return "\n".join(content)
def split_a3m(self, limits):
new_a3m = A3M_Container()
if self.consensus:
new_consensus_sequence = self.get_sub_sequence(self.consensus[1],
limits)
new_a3m.consensus = (self.consensus[0], new_consensus_sequence)
for (header, sequence) in self.sequences:
new_sequence = self.get_sub_sequence(sequence, limits)
new_a3m.sequences.append((header, new_sequence))
return new_a3m
def read_a3m(self, fh):
lines = fh.readlines()
self.read_a3m_from_lines(lines)
fh.close()
def read_a3m_from_lines(self, lines):
sequence_header = None
sequence = []
is_first_line = True
for line in lines:
line = line.strip()
if len(line) == 0:
continue
elif line[0] == "#":
if is_first_line:
self.header = line
elif line[0] == ">":
if sequence_header:
self.check_and_add_sequence(sequence_header,
"".join(sequence))
sequence = []
sequence_header = line.rstrip()
else:
sequence.append(line.strip().strip("\x00"))
is_first_line = False
if sequence_header:
self.check_and_add_sequence(sequence_header, "".join(sequence))
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