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Commit 4d65fea6 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Doc and style fixes in HHblits binding.

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modules/bindings/doc/hhblits.rst
+ 1
− 14
View file @ 4d65fea6
......@@ -109,20 +109,7 @@ so one may want to extract them:
Binding API
--------------------------------------------------------------------------------
.. autoclass:: ost.bindings.hhblits.HHblits
.. automodule:: ost.bindings.hhblits
:members:
.. autoclass:: ost.bindings.hhblits.HHblitsHit
.. autoclass:: ost.bindings.hhblits.HHblitsHeader
.. autofunction:: ost.bindings.hhblits.ParseHHblitsOutput
.. autofunction:: ost.bindings.hhblits.ParseA3M
.. autofunction:: ost.bindings.hhblits.ParseHeaderLine
.. autofunction:: ost.bindings.hhblits.ParseHHM
.. autofunction:: ost.bindings.hhblits.EstimateMemConsumption
.. LocalWords: HHblits homologs
modules/bindings/pymod/hhblits.py
+ 72
− 68
View file @ 4d65fea6
'''HHblits wrapper.
'''HHblits wrapper classes and functions.
'''
import subprocess
......@@ -124,8 +124,8 @@ def ParseHeaderLine(line):
:param line: Line from the output header.
:type line: :class:`str`
:return: Hit information
:rtype: :class:`HHblitsHit`
: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():
......@@ -147,15 +147,14 @@ def ParseHeaderLine(line):
def ParseHHblitsOutput(output):
"""
Parses the HHblits output and returns a tuple of :class:`HHblitsHeader` and
a list of :class:`HHblitsHit` instances.
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: output of a :meth:`HHblits.Search`, needs to be iteratable,
e.g. an open file handle
:type output: :class:`file`/ iteratable
: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:`HHblitsHit`)
:rtype: (:class:`HHblitsHeader`, :class:`list` of :class:`HHblitsHit`)
"""
lines = iter(output)
def _ParseHeaderSection(lines):
......@@ -271,10 +270,10 @@ def ParseHHblitsOutput(output):
def ParseA3M(a3m_file):
'''
Parse secondary structure information and the multiple sequence alignment
out of an A3M file.
out of an A3M file as produced by :meth:`HHblits.BuildQueryMSA`.
:param a3m_file: Iteratable containing the lines of the A3M file
:type a3m_file: iteratable, e.g. an opened file
: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`).
......@@ -323,36 +322,36 @@ def ParseA3M(a3m_file):
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)
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))
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.
'''
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" (~ost.seq.SequenceHandle).
"consensus" (:class:`~ost.seq.SequenceHandle`).
'''
profile_dict = dict()
state = 'NONE'
......@@ -423,9 +422,8 @@ def ParseHHM(profile):
seq.CreateSequence(msa_head[i], ts))
al.append(nl)
profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
al,
seq.CreateSequence(msa_head[0], t))
#print profile_dict['msa'].ToString(80)
al, seq.CreateSequence(msa_head[0], t))
#print profile_dict['msa'].ToString(80)
# Consensus
profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
......@@ -501,28 +499,23 @@ class HHblits:
self.working_dir = tmp_dir.dirname
self.filename = tmp_dir.files[0]
def Cleanup(self):
"""Delete temporary data.
def BuildQueryMSA(self, nrdb, iterations=1, mact=None, cpu=1):
"""Builds the MSA for the query sequence.
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)
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.
def BuildQueryMSA(self, nrdb, iterations=1, mact=None, cpu=1):
"""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. hhblits does **not** call PSIPRED on the
MSA to predict the secondary structure of the query sequence. This is
done by addss.pl of hhtools. The predicted secondary structure is
stored together with the sequences identified by hhblits.
hhblits does **not** call PSIPRED on the MSA to predict the secondary
structure of the query sequence. This is done by addss.pl of hhtools.
The predicted secondary structure is stored together with the sequences
identified by hhblits.
The produced A3M file can be parsed by :func:`ParseA3M`.
:param nrdb: Database to be align against; has to be an hhblits database
:type nrdb: :class:`str`
......@@ -536,7 +529,7 @@ class HHblits:
:param cpu: ``-cpu`` of hhblits
:type cpu: :class:`int`
:return: the path to the MSA file
:return: The path to the A3M file containing the MSA
:rtype: :class:`str`
"""
a3m_file = '%s.a3m' % os.path.splitext(self.filename)[0]
......@@ -588,13 +581,15 @@ class HHblits:
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.
:param a3m_file: input MSA
The produced A3M file can be parsed by :func:`ParseA3M`.
:param a3m_file: Path to input MSA as produced by :meth:`BuildQueryMSA`
:type a3m_file: :class:`str`
:param hhm_file: output file name
:param hhm_file: Desired output file name
:type hhm_file: :class:`str`
:return: the path to the profile
:return: Path to the profile file
:rtype: :class:`str`
"""
hhmake = os.path.join(self.bin_dir, 'hhmake')
......@@ -609,7 +604,6 @@ class HHblits:
raise IOError('could not convert a3m to hhm file')
return hhm_file
def A3MToCS(self, a3m_file, cs_file=None, options={}):
"""
Converts the A3M alignment file to a column state sequence file. If
......@@ -657,8 +651,19 @@ class HHblits:
ost.LogWarning('Creating column state sequence file (%s) failed' % \
cs_file)
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
......@@ -667,11 +672,10 @@ class HHblits:
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`.
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: input MSA file
:type a3m_file: :class:`str`
......@@ -708,7 +712,7 @@ class HHblits:
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'%(
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),
hhr_file,
......@@ -730,12 +734,12 @@ class HHblits:
return hhr_file
__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader', 'ParseHeaderLine',
__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader',
'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
'EstimateMemConsumption']
'ParseHeaderLine', 'EstimateMemConsumption']
# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str mact
# LocalWords: cpu hhm func ParseHHblitsOutput ss pred conf msa hhsuite dir
# LocalWords: attr basename rtype cstranslate tuple HHblitsHeader meth aln
# LocalWords: HHblitsHit iteratable evalue pvalue neff hmms datetime
# LocalWords: HHblitsHit iterable evalue pvalue neff hmms datetime
# LocalWords: whitespace whitespaces
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