'''HHblits wrapper classes and functions.
'''
import subprocess
import datetime
import os
import shutil
import tempfile
import ost
from ost import settings, seq
from ost.bindings import utils
class HHblitsHit:
"""
A hit found by HHblits
.. attribute:: hit_id
String identifying the hit
:type: :class:`str`
.. attribute:: aln
Pairwise alignment containing the aligned part between the query and the
target. First sequence is the query, the second sequence the target.
:type: :class:`~ost.seq.AlignmentHandle`
.. attribute:: score
The alignment score
:type: :class:`float`
.. attribute:: ss_score
The secondary structure score
:type: :class:`float`
.. attribute:: evalue
The E-value of the alignment
:type: :class:`float`
.. attribute:: pvalue
The P-value of the alignment
:type: :class:`float`
.. attribute:: prob
The probability of the alignment (between 0 and 100)
:type: :class:`float`
"""
def __init__(self, hit_id, aln, score, ss_score, evalue, pvalue, prob):
self.hit_id = hit_id
self.aln = aln
self.score = score
self.ss_score = ss_score
self.evalue = evalue
self.prob = prob
self.pvalue = pvalue
class HHblitsHeader:
"""Stats from the beginning of search output.
.. attribute:: query
The name of the query sequence
:type: :class:`str`
.. attribute:: match_columns
Total of aligned Match columns
:type: :class:`int`
.. attribute:: n_eff
Value of the ``-neff`` option
:type: :class:`float`
.. attribute:: searched_hmms
Number of profiles searched
:type: :class:`int`
.. attribute:: date
Execution date
:type: :class:`datetime.datetime`
.. attribute:: command
Command used to run
:type: :class:`str`
"""
def __init__(self):
self.query = ''
self.match_columns = 0
self.n_eff = 0
self.searched_hmms = 0
self.date = None
self.command = ''
def ParseHeaderLine(line):
'''Fetch header content.
First, we seek the start of the identifier, that is, the first whitespace
after the hit number + 1. Since the identifier may contain whitespaces
itself, we cannot split the whole line
:param line: Line from the output header.
:type line: :class:`str`
:return: Hit information and query/template offsets
:rtype: (:class:`HHblitsHit`, (:class:`int`, :class:`int`))
'''
for i in range(0, len(line)):
if line[i].isdigit():
break
for i in range(i, len(line)):
if line[i] == ' ':
break
assert len(line)-i >= 31 and line[i+1] != ' '
hit_id = line[i+1:i+31].strip()
fields = line[i+32:].split()
prob = float(fields[0])
evalue = float(fields[1])
pvalue = float(fields[2])
score = float(fields[3])
ss_score = float(fields[4])
offsets = (int(fields[6].split('-')[0]), int(fields[7].split('-')[0]))
return (HHblitsHit(hit_id, None, score, ss_score, evalue, pvalue, prob),
offsets)
def ParseHHblitsOutput(output):
"""
Parses the HHblits output as produced by :meth:`HHblits.Search` and returns
the header of the search results and a list of hits.
:param output: Iterable containing the lines of the HHblits output file
:type output: iterable (e.g. an open file handle)
:return: a tuple of the header of the search results and the hits
:rtype: (:class:`HHblitsHeader`, :class:`list` of :class:`HHblitsHit`)
"""
lines = iter(output)
def _ParseHeaderSection(lines):
value_start_column = 14
date_pattern = '%a %b %d %H:%M:%S %Y'
header = HHblitsHeader()
line = next(lines)
assert line.startswith('Query')
header.query = line[value_start_column:].strip()
line = next(lines)
assert line.startswith('Match_columns')
header.match_columns = int(line[value_start_column:].strip())
line = next(lines)
assert line.startswith('No_of_seqs')
line = next(lines)
assert line.startswith('Neff')
header.n_eff = float(line[value_start_column:].strip())
line = next(lines)
assert line.startswith('Searched_HMMs')
header.searched_hmms = int(line[value_start_column:].strip())
line = next(lines)
assert line.startswith('Date')
value = line[value_start_column:].strip()
header.date = datetime.datetime.strptime(value, date_pattern)
line = next(lines)
assert line.startswith('Command')
header.command = line[value_start_column:].strip()
line = next(lines)
assert len(line.strip()) == 0
return header
def _ParseTableOfContents(lines):
line = next(lines)
assert line.startswith(' No Hit')
hits = []
while True:
line = next(lines)
if len(line.strip()) == 0:
return hits
hits.append(ParseHeaderLine(line))
return hits
def _ParseResultBody(query_id, hits, lines):
entry_index = None
query_str = ''
templ_str = ''
def _MakeAln(query_id, hit_id, query_string, templ_string,
q_offset, t_offset):
s1 = seq.CreateSequence(query_id, query_string)
s1.offset = q_offset-1
s2 = seq.CreateSequence(hit_id, templ_string)
s2.offset = t_offset-1
return seq.CreateAlignment(s1, s2)
try:
while True:
# Lines which we are interested in:
# - "Done!" -> end of list
# - "No ..." -> next item in list
# - "T <hit_id> <start> <data> <end>"
# - "Q <query_id> <start> <data> <end>"
# -> rest is to be skipped
line = next(lines)
if len(line.strip()) == 0:
continue
if line.startswith('Done!'):
if len(query_str) > 0:
hits[entry_index][0].aln = _MakeAln(\
query_id, hits[entry_index][0].hit_id,
query_str, templ_str, *hits[entry_index][1])
return [h for h, o in hits]
if line.startswith('No '):
if len(query_str) > 0:
hits[entry_index][0].aln = _MakeAln(\
query_id, hits[entry_index][0].hit_id,
query_str, templ_str, *hits[entry_index][1])
entry_index = int(line[3:].strip())-1
line = next(lines)
hits[entry_index][0].hit_id = line[1:].strip()
query_str = ''
templ_str = ''
# skip the next line. It doesn't contain information we
# don't already know
next(lines)
continue
assert entry_index != None
# Skip all "T ..." and "Q ..." lines besides the one we want
if line[1:].startswith(' Consensus'):
continue
if line[1:].startswith(' ss_pred'):
continue
if line[1:].startswith(' ss_conf'):
continue
if line[1:].startswith(' ss_dssp'):
continue
if line.startswith('T '):
for start_pos in range(22, len(line)):
if line[start_pos].isalpha() or line[start_pos] == '-':
break
end_pos = line.find(' ', start_pos)
# this can fail if we didn't skip all other "T ..." lines
if end_pos == -1:
error_str = "Unparsable line '%s' for entry No %d" \
% (line.strip(), entry_index + 1)
raise AssertionError(error_str)
templ_str += line[start_pos:end_pos]
if line.startswith('Q '):
for start_pos in range(22, len(line)):
if line[start_pos].isalpha() or line[start_pos] == '-':
break
end_pos = line.find(' ', start_pos)
# this can fail if we didn't skip all other "Q ..." lines
if end_pos == -1:
error_str = "Unparsable line '%s' for entry No %d" \
% (line.strip(), entry_index + 1)
raise AssertionError(error_str)
query_str += line[start_pos:end_pos]
except StopIteration:
if len(query_str) > 0:
hits[entry_index][0].aln = _MakeAln(query_id,
hits[entry_index][0].hit_id,
query_str, templ_str,
*hits[entry_index][1])
return [h for h, o in hits]
header = _ParseHeaderSection(lines)
# parse the table of contents. This is neccessary as some of the properties
# (i.e. start of alignment) we need are only given there. From the TOC we
# create a list of hits that is then further filled with data when we parse
# the actual result body
hits = _ParseTableOfContents(lines)
return header, _ParseResultBody(header.query, hits, lines)
def ParseA3M(a3m_file):
'''
Parse secondary structure information and the multiple sequence alignment
out of an A3M file as produced by :meth:`HHblits.BuildQueryMSA`.
:param a3m_file: Iterable containing the lines of the A3M file
:type a3m_file: iterable (e.g. an open file handle)
:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
(:class:`list`) and "msa" (:class:`~ost.seq.AlignmentHandle`).
If not available, "ss_pred" and "ss_conf" entries are set to None.
'''
profile_dict = dict()
state = 'NONE'
pred_seq_txt = ''
conf_seq_txt = ''
msa_seq = list()
msa_head = list()
for line in a3m_file:
if len(line.rstrip()) == 0:
continue
elif line.startswith('>ss_pred'):
state = 'sspred'
continue
elif line.startswith('>ss_conf'):
state = 'ssconf'
continue
elif line[0] == '>':
msa_seq.append('')
msa_head.append(line[1:].rstrip())
state = 'msa'
continue
if state == 'sspred':
pred_seq_txt += line.rstrip()
elif state == 'ssconf':
conf_seq_txt += line.rstrip()
elif state == 'msa':
msa_seq[len(msa_seq)-1] += line.rstrip()
if len(pred_seq_txt) > 0:
profile_dict['ss_pred'] = list()
profile_dict['ss_conf'] = list()
for i in range(0, len(pred_seq_txt)):
profile_dict['ss_pred'].append(pred_seq_txt[i])
profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
else:
profile_dict['ss_pred'] = None
profile_dict['ss_conf'] = None
# post processing
# MSA
profile_dict['msa'] = None
if len(msa_seq) > 1:
t = msa_seq[0]
al = seq.AlignmentList()
for i in range(1, len(msa_seq)):
qs = ''
ts = ''
k = 0
for c in msa_seq[i]:
if c.islower():
qs += '-'
ts += c.upper()
else:
qs += t[k]
ts += c
k += 1
nl = seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
seq.CreateSequence(msa_head[i], ts))
al.append(nl)
profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
al, seq.CreateSequence(msa_head[0], t))
return profile_dict
def ParseHHM(profile):
'''
Parse secondary structure information and the MSA out of an HHM profile as
produced by :meth:`HHblits.A3MToProfile`.
:param profile: Opened file handle holding the profile.
:type profile: :class:`file`
:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
(:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
"consensus" (:class:`~ost.seq.SequenceHandle`).
If not available, "ss_pred" and "ss_conf" entries are set to None.
'''
profile_dict = dict()
state = 'NONE'
pred_seq_txt = ''
conf_seq_txt = ''
consensus_txt = ''
msa_seq = list()
msa_head = list()
for line in profile:
if len(line.rstrip()) == 0:
continue
if line.rstrip() == '>ss_pred PSIPRED predicted secondary structure':
state = 'sspred'
continue
elif line.rstrip() == '>ss_conf PSIPRED confidence values':
state = 'ssconf'
continue
elif line.rstrip() == '>Consensus':
state = 'consensus'
continue
elif line[0] == '>':
if state == 'consensus' or state == 'msa':
msa_seq.append('')
msa_head.append(line[1:].rstrip())
else:
raise IOError('Profile file "%s" is missing ' % profile.name+
'the "Consensus" section')
state = 'msa'
continue
elif line[0] == '#':
state = 'NONE'
continue
if state == 'sspred':
pred_seq_txt += line.rstrip()
elif state == 'ssconf':
conf_seq_txt += line.rstrip()
elif state == 'msa':
msa_seq[len(msa_seq)-1] += line.rstrip()
elif state == 'consensus':
consensus_txt += line.rstrip()
if len(pred_seq_txt) > 0:
profile_dict['ss_pred'] = list()
profile_dict['ss_conf'] = list()
for i in range(0, len(pred_seq_txt)):
profile_dict['ss_pred'].append(pred_seq_txt[i])
profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
else:
profile_dict['ss_pred'] = None
profile_dict['ss_conf'] = None
# post processing
# MSA
profile_dict['msa'] = None
if len(msa_seq):
t = msa_seq[0]
al = seq.AlignmentList()
for i in range(1, len(msa_seq)):
qs = ''
ts = ''
k = 0
for c in msa_seq[i]:
if c.islower():
qs += '-'
ts += c.upper()
else:
qs += t[k]
ts += c
k += 1
nl = seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
seq.CreateSequence(msa_head[i], ts))
al.append(nl)
profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
al, seq.CreateSequence(msa_head[0], t))
# Consensus
profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
return profile_dict
class HHblits:
"""
Initialise a new HHblits "search" for the given query. Query may either
be a :class:`~ost.seq.SequenceHandle` or a string. In the former case, the
query is the actual query sequence, in the latter case, the query is the
filename to the file containing the query.
:param query: Query sequence as file or sequence.
:type query: :class:`~ost.seq.SequenceHandle` or :class:`str`
:param hhsuite_root: Path to the top-level directory of your hhsuite
installation.
:type hhsuite_root: :class:`str`
:param hhblits_bin: Name of the hhblits binary. Will only be used if
:attr:`hhsuite_root`:file:`/bin/hhblits` does not exist.
:type hhblits_bin: :class:`str`
:param working_dir: Directory for temporary files. Will be created if not
present but **not** automatically deleted.
:type working_dir: :class:`str`
"""
OUTPUT_PREFIX = 'query_hhblits'
def __init__(self, query, hhsuite_root, hhblits_bin=None, working_dir=None):
self.query = query
self.hhsuite_root = hhsuite_root
if os.path.exists(os.path.join(self.hhsuite_root, 'bin/hhblits')):
self.bin_dir = os.path.join(self.hhsuite_root, 'bin')
self.hhblits_bin = os.path.join(self.hhsuite_root, 'bin/hhblits')
else:
self.hhblits_bin = settings.Locate('hhblits',
explicit_file_name=hhblits_bin)
self.bin_dir = os.path.dirname(self.hhblits_bin)
# guess root folder (note: this may fail in future)
self.hhsuite_root = os.path.dirname(self.bin_dir)
if working_dir:
self.needs_cleanup = False
self.working_dir = working_dir
if not os.path.exists(working_dir):
os.mkdir(working_dir)
if isinstance(query, str):
self.filename = os.path.abspath(os.path.join(
self.working_dir, os.path.basename(query)))
if self.filename != os.path.abspath(query):
shutil.copy(query, self.filename)
else:
self.filename = os.path.join(self.working_dir,
'%s.fasta' % HHblits.OUTPUT_PREFIX)
ost.io.SaveSequence(query, self.filename)
else:
self.needs_cleanup = True
if isinstance(query, str):
self.working_dir = tempfile.mkdtemp()
self.filename = os.path.abspath(os.path.join(
self.working_dir, os.path.basename(query)))
shutil.copy(query, self.filename)
else:
tmp_dir = utils.TempDirWithFiles((query,))
self.working_dir = tmp_dir.dirname
self.filename = tmp_dir.files[0]
def BuildQueryMSA(self, nrdb, options={}, a3m_file=None, assign_ss=True):
"""Builds the MSA for the query sequence.
This function directly uses hhblits of hhtools. While in theory it would
be possible to do this by PSI-blasting on our own, hhblits is supposed
to be faster. Also it is supposed to prevent alignment corruption. The
alignment corruption is caused by low-scoring terminal alignments that
draw the sequences found by PSI-blast away from the optimum. By removing
these low scoring ends, part of the alignment corruption can be
suppressed.
The produced A3M file can be parsed by :func:`ParseA3M`. If the file was
already produced, hhblits is not called again and the existing file path
is returned (neglecting the *assign_ss* flag!!!).
:param nrdb: Database to be align against; has to be an hhblits database
:type nrdb: :class:`str`
:param options: Dictionary of options to *hhblits*, one "-" is added in
front of every key. Boolean True values add flag without
value. Merged with default options
{'cpu': 1, 'n': 1, 'e': 0.001}, where 'n' defines the
number of iterations.
:type options: :class:`dict`
:param a3m_file: a path of a3m_file to be used, optional
:type a3m_file: :class:`str`
:param assign_ss: HHblits does not assign predicted secondary structure
by default. You can optionally assign it with the
addss.pl script provided by the HH-suite. However,
your HH-suite installation requires you to specify
paths to PSIRED etc. We refer to the HH-suite user
guide for further instructions.
:type assign_ss: :class:`bool`
:return: The path to the A3M file containing the MSA
:rtype: :class:`str`
"""
if a3m_file is None:
a3m_file = '%s.a3m' % os.path.splitext(self.filename)[0]
else:
a3m_file = os.path.abspath(a3m_file)
if os.path.exists(a3m_file):
ost.LogInfo('Reusing already existing query alignment (%s)' % a3m_file)
return a3m_file
ost.LogInfo('Using hhblits from "%s"' % self.hhsuite_root)
full_nrdb = os.path.join(os.path.abspath(os.path.split(nrdb)[0]),
os.path.split(nrdb)[1])
# create MSA
opts = {'cpu' : 1, # no. of cpus used
'n' : 1, # no. of iterations
'e' : 0.001} # evalue threshold
opts.update(options)
opt_cmd, _ = _ParseOptions(opts)
hhblits_cmd = '%s -i %s -oa3m %s -d %s %s' % \
(self.hhblits_bin, self.filename, a3m_file, full_nrdb,
opt_cmd)
p = subprocess.run(hhblits_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
lines = p.stdout.decode().splitlines()
for line in lines:
ost.LogVerbose(line.strip())
lines = p.stderr.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
if not os.path.exists(a3m_file):
raise RuntimeError('Building query profile failed, no output')
if assign_ss:
return self.AssignSSToA3M(a3m_file)
else:
return a3m_file
def AssignSSToA3M(self, a3m_file):
"""
HHblits does not assign predicted secondary structure by default.
You can optionally assign it with the addss.pl script provided by the
HH-suite. However, your HH-suite installation requires you to specify
paths to PSIRED etc. We refer to the HH-suite user guide for further
instructions.
:param a3m_file: Path to file you want to assign secondary structure to
:type a3m_file: :class:`str`
"""
a3m_file = os.path.abspath(a3m_file)
addss_cmd = "perl %s %s" % (os.path.join(self.hhsuite_root,
'scripts/addss.pl'),
a3m_file)
env = dict(os.environ)
env.update({'PERL5LIB' : os.path.join(self.hhsuite_root, 'scripts'),
'HHLIB' : os.path.join(self.hhsuite_root),
'PATH' : '%s:%s' % (os.path.join(self.hhsuite_root, 'bin'),
os.environ['PATH'])})
p = subprocess.run(addss_cmd, shell=True, cwd=self.working_dir,
env=env, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
lines = p.stdout.decode().splitlines()
for line in lines:
ost.LogVerbose(line.strip())
if 'error' in line.lower() or 'bad interpreter' in line.lower():
raise RuntimeError('Predicting secondary structure for MSA '+
'(%s) failed, on command: %s' % (a3m_file, line))
lines = p.stderr.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
if 'error' in line.lower() or 'bad interpreter' in line.lower():
raise RuntimeError('Predicting secondary structure for MSA '+
'(%s) failed, on command: %s' % (a3m_file, line))
return a3m_file
def A3MToProfile(self, a3m_file, hhm_file=None):
"""
Converts the A3M alignment file to a hhm profile. If hhm_file is not
given, the output file will be set to <:attr:`a3m_file`-basename>.hhm.
The produced HHM file can be parsed by :func:`ParseHHM`.
If the file was already produced, the existing file path is returned
without recomputing it.
:param a3m_file: Path to input MSA as produced by :meth:`BuildQueryMSA`
:type a3m_file: :class:`str`
:param hhm_file: Desired output file name
:type hhm_file: :class:`str`
:return: Path to the profile file
:rtype: :class:`str`
"""
hhmake = os.path.join(self.bin_dir, 'hhmake')
if not hhm_file:
hhm_file = '%s.hhm' % os.path.splitext(a3m_file)[0]
if os.path.exists(hhm_file):
return hhm_file
ost.LogVerbose('converting %s to %s' % (a3m_file, hhm_file))
p = subprocess.run('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
shell=True, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
lines = p.stdout.decode().splitlines()
for line in lines:
ost.LogVerbose(line.strip())
lines = p.stderr.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
if p.returncode != 0:
raise IOError('could not convert a3m to hhm file')
if not os.path.exists(hhm_file):
raise RuntimeError('could not convert a3m to hhm file, no output')
return hhm_file
def A3MToCS(self, a3m_file, cs_file=None, options={}):
"""
Converts the A3M alignment file to a column state sequence file. If
cs_file is not given, the output file will be set to
<:attr:`a3m_file`-basename>.seq219.
If the file was already produced, the existing file path is returned
without recomputing it.
:param a3m_file: Path to input MSA as produced by :meth:`BuildQueryMSA`
:type a3m_file: :class:`str`
:param cs_file: Output file name (may be omitted)
:type cs_file: :class:`str`
:param options: Dictionary of options to *cstranslate*, one "-" is added
in front of every key. Boolean True values add flag
without value.
:type options: :class:`dict`
:return: Path to the column state sequence file
:rtype: :class:`str`
"""
cstranslate = os.path.join(self.bin_dir, 'cstranslate')
if not cs_file:
cs_file = '%s.seq219' % os.path.splitext(a3m_file)[0]
if os.path.exists(cs_file):
return cs_file
opt_cmd, _ = _ParseOptions(options)
cs_cmd = '%s -i %s -o %s %s' % (
cstranslate,
os.path.abspath(a3m_file),
os.path.abspath(cs_file),
opt_cmd)
ost.LogVerbose('converting %s to %s' % (a3m_file, cs_file))
p = subprocess.run(cs_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if not os.path.exists(cs_file):
raise RuntimeError('Creating column state sequence file failed, ' +
'no output')
if b'Wrote abstract state sequence to' in p.stdout:
return cs_file
else:
raise RuntimeError('Creating column state sequence file failed')
def Cleanup(self):
"""Delete temporary data.
Delete temporary data if no working dir was given. Controlled by
:attr:`needs_cleanup`.
"""
if self.needs_cleanup and os.path.exists(self.working_dir):
shutil.rmtree(self.working_dir)
def CleanupFailed(self):
'''In case something went wrong, call to make sure everything is clean.
This will delete the working dir independently of :attr:`needs_cleanup`.
'''
store_needs_cleanup = self.needs_cleanup
self.needs_cleanup = True
self.Cleanup()
self.needs_cleanup = store_needs_cleanup
def Search(self, a3m_file, database, options={}, prefix=''):
"""
Searches for templates in the given database. Before running the search,
the hhm file is copied. This makes it possible to launch several hhblits
instances at once. Upon success, the filename of the result file is
returned. This file may be parsed with :func:`ParseHHblitsOutput`.
:param a3m_file: Path to input MSA as produced by :meth:`BuildQueryMSA`
:type a3m_file: :class:`str`
:param database: Search database, needs to be the common prefix of the
database files
:type database: :class:`str`
:param options: Dictionary of options to *hhblits*, one "-" is added in
front of every key. Boolean True values add flag without
value. Merged with default options {'cpu': 1, 'n': 1},
where 'n' defines the number of iterations.
:type options: :class:`dict`
:param prefix: Prefix to the result file
:type prefix: :class:`str`
:return: The path to the result file
:rtype: :class:`str`
"""
opts = {'cpu' : 1, # no. of cpus used
'n' : 1} # no. of iterations
opts.update(options)
opt_cmd, opt_str = _ParseOptions(opts)
base = os.path.basename(os.path.splitext(a3m_file)[0])
hhr_file = '%s%s_%s.hhr' % (prefix, base, opt_str)
hhr_file = os.path.join(self.working_dir, hhr_file)
search_cmd = '%s %s -e 0.001 -Z 10000 -B 10000 -i %s -o %s -d %s' % (
self.hhblits_bin,
opt_cmd,
os.path.abspath(a3m_file),
os.path.abspath(hhr_file),
os.path.join(os.path.abspath(os.path.split(database)[0]),
os.path.split(database)[1]))
ost.LogInfo('searching %s' % database)
ost.LogVerbose(search_cmd)
p = subprocess.run(search_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
lines = p.stdout.decode().splitlines()
for line in lines:
ost.LogVerbose(line.strip())
lines = p.stderr.decode().splitlines()
for line in lines:
ost.LogError(line.strip())
if p.returncode != 0:
raise RuntimeError('Sequence search failed')
if not os.path.exists(hhr_file):
raise RuntimeError('Sequence search failed, no output')
return hhr_file
def _ParseOptions(opts):
"""
:return: Tuple of strings (opt_cmd, opt_str), where opt_cmd can be
passed to command ("-" added in front of keys, options
separated by space) and opt_str (options separated by "_")
can be used for filenames.
:param opts: Dictionary of options, one "-" is added in front of every
key. Boolean True values add flag without value.
"""
opt_cmd = list()
opt_str = list()
for k, val in opts.items():
if type(val) == type(True):
if val == True:
opt_cmd.append('-%s' % str(k))
opt_str.append(str(k))
else:
opt_cmd.append('-%s %s' % (str(k), str(val)))
opt_str.append('%s%s' % (str(k), str(val)))
opt_cmd = ' '.join(opt_cmd)
opt_str = '_'.join(opt_str)
return opt_cmd, opt_str
__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader',
'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
'ParseHeaderLine']
# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str
# LocalWords: cpu hhm func ParseHHblitsOutput ss pred conf msa hhsuite dir
# LocalWords: attr basename rtype cstranslate tuple HHblitsHeader meth aln
# LocalWords: HHblitsHit iterable evalue pvalue neff hmms datetime
# LocalWords: whitespace whitespaces