diff --git a/modules/bindings/doc/hhblits.rst b/modules/bindings/doc/hhblits.rst
index c822d5bd0641d1fc6a863066f4196e3fe77f467a..fd1fca05b0e33e0bf7e77807776b43da7102a547 100644
--- a/modules/bindings/doc/hhblits.rst
+++ b/modules/bindings/doc/hhblits.rst
@@ -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
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index dddaa7404688f414eaa1a3915c6141b049ff52ce..7ad416987d9959e6047ae07ade6436db94e075ec 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -1,4 +1,4 @@
-'''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