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"""
Author: Marco Biasini
"""
import re
from ost import seq
class HHSearchHit:
def __init__(self, summary, alignment):
self.summary=summary
self.alignment=alignment
class HitSummary:
def __init__(self, pdb_id, chain, prob, e_value, query_start, query_end,
template_start, template_end):
self.prob=prob
self.pdb_id=pdb_id
self.chain=chain
self.e_value=e_value
self.query_start=query_start
self.query_end=query_end
self.template_start=template_start
self.template_end=template_end
class HHSearchResult:
"""
Read HHSearch result file. The result is stored in a list of hh search hits.
Usage:
result=HHSearchResult('output.hhr')
for hit in result.hits:
print hit.pdb_id, hit.chain
print hit.alignment.ToString(80)
"""
def __init__(self, filename, pipe_separated=False):
self.pipe_separated=pipe_separated
self._Read(filename)
def _Read(self, filename):
ifile=open(filename)
self._ReadHeader(ifile)
summaries=self._ReadHitSummaries(ifile)
self.hits=self._ReadHitDetails(ifile, summaries)
def _ReadHeader(self, ifile):
header_lines=[]
for line in ifile:
stripped_line=line.strip()
if stripped_line=='':
break
header_lines.append(stripped_line)
for header_line in header_lines:
var, value=re.split('\s+', header_line, 1)
setattr(self, var.lower(), value)
def _ReadHitSummaries(self, ifile):
summary_lines=[]
skip_header=True
for line in ifile:
if skip_header==True:
skip_header=False
continue
stripped_line=line.strip()
if stripped_line=='':
break
summary_lines.append(line)
summaries=[]
for summary_line in summary_lines:
pdb_id, chain=(None, None)
if self.pipe_separated:
parts=summary_line[4:37].split('|')
pdb_id=parts[1][:4]
chain=parts[1][4]
else:
pdb_id=summary_line[4:8]
chain=summary_line[9]
prob=float(summary_line[36:40])
e_value=0.0
query_range=summary_line[76:84].split('-')
query_start=int(query_range[0].strip())
query_end=int(query_range[1].strip())
template_range=summary_line[86:94].split('-')
template_start=int(template_range[0].strip())
template_end=int(template_range[1].strip())
summaries.append(HitSummary(pdb_id, chain, prob, e_value, query_start,
query_end, template_start, template_end))
return summaries
def _ReadHitDetails(self, ifile, summaries):
hits=[]
for summary in summaries:
alignment=self._ReadHitDetail(ifile)
hits.append(HHSearchHit(summary, alignment))
return hits
def _ReadHitDetail(self, ifile):
skip_header=True
q_seq, t_seq=('', '')
for line in ifile:
if skip_header==True:
if line.startswith('>'):
skip_header=False
continue
if line.startswith('No'):
break
if line.strip()=='':
continue
if line.startswith('Q ss_pred') or line.startswith('Q Consensus'):
continue
if line.startswith('T ss_pred') or line.startswith('T Consensus'):
continue
if line.startswith(' '):
continue
if line.startswith('Q'):
q_seq+=re.split('\s+', line)[3]
if line.startswith('T'):
t_seq+=re.split('\s+', line)[3]
ali=seq.AlignmentHandle()
ali.AddSequence(seq.Sequence.FromString('query', q_seq))
ali.AddSequence(seq.Sequence.FromString('target', t_seq))
return ali
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