Public Member Functions | |
def | __init__ |
def | Cleanup |
def | BuildQueryMSA |
def | A3MToProfile |
def | A3MToCS |
def | CleanupFailed |
def | Search |
Data Fields | |
query | |
hhsuite_root | |
bin_dir | |
hhblits_bin | |
hhlib_dir | |
needs_cleanup | |
working_dir | |
filename | |
Static Public Attributes | |
string | OUTPUT_PREFIX = 'query_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`
Definition at line 446 of file hhblits.py.
def __init__ | ( | self, | ||
query, | ||||
hhsuite_root, | ||||
hhblits_bin = None , |
||||
working_dir = None | ||||
) |
Definition at line 467 of file hhblits.py.
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. :param a3m_file: A3M file to be converted :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*, must come with the right amount of '-' in front. :type options: :class:`dict` :return: the path to the column state sequence file :rtype: :class:`str`
Definition at line 613 of file hhblits.py.
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. :param a3m_file: input MSA :type a3m_file: :class:`str` :param hhm_file: output file name :type hhm_file: :class:`str` :return: the path to the profile :rtype: :class:`str`
Definition at line 586 of file hhblits.py.
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. :param nrdb: Database to be align against; has to be an hhblits database :type nrdb: :class:`str` :param iterations: Number of hhblits iterations :type iterations: :class:`int` :param mact: ``-mact`` of hhblits :type mact: :class:`float` :param cpu: ``-cpu`` of hhblits :type cpu: :class:`int` :return: the path to the MSA file :rtype: :class:`str`
Definition at line 513 of file hhblits.py.
def Cleanup | ( | self | ) |
Delete temporary data. Delete temporary data if no working dir was given. Controlled by :attr:`needs_cleanup`.
Definition at line 504 of file hhblits.py.
def CleanupFailed | ( | self | ) |
In case something went wrong, call to make sure everything is clean.
Definition at line 660 of file hhblits.py.
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: input MSA file :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, must come with the right amount of '-' in front. :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 668 of file hhblits.py.
Definition at line 471 of file hhblits.py.
Definition at line 484 of file hhblits.py.
Definition at line 472 of file hhblits.py.
Definition at line 477 of file hhblits.py.
Definition at line 469 of file hhblits.py.
Definition at line 479 of file hhblits.py.
string OUTPUT_PREFIX = 'query_hhblits' [static] |
Definition at line 466 of file hhblits.py.
Definition at line 468 of file hhblits.py.
Definition at line 480 of file hhblits.py.