HHblits Class Reference

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'

Detailed Description

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.

Member Function Documentation

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.