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`
Definition at line 458 of file hhblits2.py.
| def A3MToCS |
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self, |
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a3m_file, |
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cs_file = None, |
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options = {} |
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) |
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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`
Definition at line 641 of file hhblits2.py.
| def BuildQueryMSA |
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self, |
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nrdb, |
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options = {}, |
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a3m_file = None |
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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.
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.
: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},
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`
:return: The path to the A3M file containing the MSA
:rtype: :class:`str`
Definition at line 517 of file hhblits2.py.
| def Search |
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self, |
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a3m_file, |
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database, |
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options = {}, |
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prefix = '' |
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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`
Definition at line 704 of file hhblits2.py.
1.8.5