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#!/usr/bin/env python3
"""
Parser for hhr result files created with hhblits|hhsearch|hhalign -o <hhr_file>
"""
import sys
from collections import namedtuple
__author__ = 'Markus Meier (markus.meier@mpibpc.mpg.de)'
__version__ = '1.0'
__license__ = "GPL-3"
hhr_alignment = namedtuple('hhr_alignment', ['query_id', 'query_length', 'query_neff',
'template_id', 'template_length', 'template_info',
'template_neff', 'query_ali', 'template_ali',
'start', 'end', 'probability', 'evalue', 'score',
'aligned_cols', 'identity', 'similarity', 'sum_probs'])
class HHRFormatError(Exception):
def __init__(self, value):
self.value = "ERROR: "+value
def __str__(self):
return repr(self.value)
def get_sequence_name(header):
name = header.replace(">", "").split()[0]
return name
def parse_result(lines):
results = []
query_id = None
query_length = None
query_neff = None
query_seq = []
template_id = None
template_length = None
template_seq = []
template_info = None
query_start = None
query_end = None
template_start = None
template_end = None
probability = None
evalue = None
score = None
identity = None
similarity = None
template_neff = None
sum_probs = None
aligned_cols = None
skipped_ali_tags = ["ss_dssp", "ss_pred", "Consensus"]
is_alignment_section = False
for line in lines:
if(line.startswith("Query")):
query_id = line.split()[1]
elif(line.startswith("Match_columns")):
query_length = int(line.split()[1])
elif(line.startswith("Neff")):
query_neff = float(line.split()[1])
elif(is_alignment_section and (line.startswith("No") or line.startswith("Done!"))):
if query_start is not None:
result = hhr_alignment(query_id, query_length, query_neff,
template_id, template_length, template_info, template_neff,
query_seq, template_seq, (query_start, template_start),
(query_end, template_end), probability, evalue, score,
aligned_cols, identity, similarity, sum_probs)
results.append(result)
template_id = None
template_info = None
query_seq = []
template_seq = []
query_start = None
query_end = None
template_start = None
template_end = None
elif(line.startswith("Probab")):
tokens = line.split()
probability = float(tokens[0].split("=")[1])
evalue = float(tokens[1].split("=")[1])
score = float(tokens[2].split("=")[1])
aligned_cols = int(tokens[3].split("=")[1])
identity = float(tokens[4].split("=")[1].replace("%", "")) / 100.0
similarity = float(tokens[5].split("=")[1])
sum_probs = float(tokens[6].split("=")[1])
if(len(tokens) > 7):
template_neff = float(tokens[7].split("=")[1])
continue
elif(line.startswith(">")):
is_alignment_section = True
template_id = line[1:].split()[0]
template_info = line
elif(line.startswith("Q")):
tokens = line.split()
if(tokens[1] in skipped_ali_tags):
continue
try:
token_2 = tokens[2].replace("(", "").replace(")", "")
token_2 = int(token_2)
except:
raise HHRFormatError(("Converting failure of start index ({}) "
"of query alignment").format(tokens[2]))
if query_start is None:
query_start = token_2
query_start = min(query_start, token_2)
try:
token_4 = tokens[4].replace("(", "").replace(")", "")
token_4 = int(token_4)
except:
raise HHRFormatError(("Converting failure of end index ({}) "
"of query alignment").format(tokens[4]))
if query_end is None:
query_end = token_4
query_end = max(query_end, token_4)
query_seq.append(tokens[3])
elif(line.startswith("T")):
tokens = line.split()
if(tokens[1] in skipped_ali_tags):
continue
template_seq.append(tokens[3])
try:
token_2 = tokens[2].replace("(", "").replace(")", "")
token_2 = int(token_2)
except:
raise HHRFormatError(("Converting failure of start index ({}) "
"of template alignment").format(tokens[2]))
if template_start is None:
template_start = token_2
template_start = min(template_start, token_2)
try:
token_4 = tokens[4].replace("(", "").replace(")", "")
token_4 = int(token_4)
except:
raise HHRFormatError(("Converting failure of end index ({}) "
"of template alignment").format(tokens[4]))
if template_end is None:
template_end = token_4
template_end = max(template_end, token_4)
try:
token_5 = tokens[4].replace("(", "").replace(")", "")
token_5 = int(token_5)
except:
raise HHRFormatError(("Converting failure of template length ({}) "
"in template alignment").format(tokens[5]))
template_length = token_5
if(template_id is not None and query_start is not None):
result = hhr_alignment(query_id, query_length, query_neff,
template_id, template_length, template_info, template_neff,
"".join(query_seq), "".join(template_seq), (query_start, template_start),
(query_end, template_end), probability, evalue, score,
aligned_cols, identity, similarity, sum_probs)
results.append(result)
return results
def read_result(input_file):
with open(input_file) as fh:
lines = fh.readlines()
return parse_result(lines)
def main():
counter = 0
for result in read_result(sys.argv[1]):
print("Alignment " + str(counter) + "\t evalue: " + str(result.evalue) +
"\t probability: " + str(result.probability))
print(result.query_id + "\t" + str(result.start[0]) + "\t" +
result.query_ali + "\t" +
str(result.end[0]))
print(result.template_id + "\t" + str(result.start[1]) + "\t" +
result.template_ali + "\t" +
str(result.end[1]))
counter += 1
if __name__ == "__main__":
main()
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