ost::bindings::hhblits Namespace Reference

Data Structures
class	HHblitsHit
class	HHblitsHeader
class	HHblits
Functions
def	ParseHeaderLine
def	ParseHHblitsOutput
def	ParseA3M
def	ParseHHM
def	EstimateMemConsumption
Variables
list	__all__

---

Detailed Description

HHblits wrapper.

---

Function Documentation

def ost::bindings::hhblits::EstimateMemConsumption

(

)

Estimate the memory needed by HHblits. By default it uses not more than 3G.
Also for small sequences it already uses quite some memnmory (46AA, 1.48G).
And since the memory consumption could depend on the iterative search runs,
how many hits are found in each step, we just go with 4G, here.

:return: Assumed memory consumtion
:rtype: (:class:`float`, :class:`str`)

Definition at line 434 of file hhblits.py.

def ost::bindings::hhblits::ParseA3M

(

a3m_file

)

Parse secondary structure information and the multiple sequence alignment 
out of an A3M file.

:param a3m_file: Iteratable containing the lines of the A3M file
:type a3m_file: iteratable, e.g. an opened file

:return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
         (:class:`list`) and "msa" (:class:`~ost.seq.AlignmentHandle`).

Definition at line 271 of file hhblits.py.

def ost::bindings::hhblits::ParseHeaderLine

(

line

)

Fetch header content.

First, we seek the start of the identifier, that is, the first whitespace
after the hit number + 1. Since the identifier may contain whitespaces
itself, we cannot split the whole line

:param line: Line from the output header.
:type line: :class:`str`

:return: Hit information
:rtype: :class:`HHblitsHit`

Definition at line 117 of file hhblits.py.

def ost::bindings::hhblits::ParseHHblitsOutput

(

output

)

Parses the HHblits output and returns a tuple of :class:`HHblitsHeader` and
a list of :class:`HHblitsHit` instances.

:param output: output of a :meth:`HHblits.Search`, needs to be iteratable,
               e.g. an open file handle
:type output: :class:`file`/ iteratable

:return: a tuple of the header of the search results and the hits
:rtype: (:class:`HHblitsHeader`, :class:`HHblitsHit`)

Definition at line 148 of file hhblits.py.

def ost::bindings::hhblits::ParseHHM

(

profile

)

Parse secondary structure information and the MSA out of an HHM profile.

: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).

Definition at line 347 of file hhblits.py.

---

Variable Documentation

list __all__

Initial value:

['HHblits', 'HHblitsHit', 'HHblitsHeader', 'ParseHeaderLine',
           'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
           'EstimateMemConsumption']

Definition at line 733 of file hhblits.py.