Package csb :: Package bio :: Package fragments :: Module rosetta :: Class RosettaFragmentMap

Class RosettaFragmentMap

            object --+    
                     |    
core.AbstractContainer --+
                         |
                        RosettaFragmentMap

Represents a Rosetta fragment library.

Nested Classes
Inherited from `core.AbstractContainer`: `__metaclass__`

Instance Methods

__init__(self, fragments, length=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__len__(self)

source code

append(self, fragment)
Append a new RosettaFragment

source code

at(self, qrank)
Returns: a tuple of all fragments, covering the specified position.

source code

complement(self, fragment)
Append fragment to the library, if the fragment is anchored around a low-confidence position. source code

dump(self, file, builder=<class 'csb.bio.fragments.rosetta.OutputBuilder'>)
Write the library to a Rosetta fragment file.

source code

fromsource(self, accession)
Returns: a tuple of all fragments, extracted from the specified source. source code

mark_unconfident(self, rank)
Mark the specified position in the target as a low-confidence one.

source code

sort(self, field='score', reverse=False)
Sort the fragments in the library. source code

starting_at(self, qrank)
Returns: a tuple of all fragments, starting at the specified target position.

source code

Inherited from core.AbstractContainer: __bool__, __getitem__, __iter__, __nonzero__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

RosettaFragmentMap

read(file, top=None)
Read a standard fragment file.

source code

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
	size
	sources
	start_positions
	unconfident_positions
Inherited from `object`: `__class__`

Method Details

init(self, fragments, length=None)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

fragments (iterable of RosettaFragment) - library fragments
length (int) - target sequence's length. If not defined, the qend of the last fragment will be used instead.

Overrides: object.__init__

(inherited documentation)

len(self)
(Length operator)

source code

Overrides: core.AbstractContainer.__len__

at(self, qrank)

source code

Parameters:

qrank (int) - position in target, rank

Returns:

a tuple of all fragments, covering the specified position.

complement(self, fragment)

source code

Append fragment to the library, if the fragment is anchored around a low-confidence position.

Parameters:

fragment (RosettaFragment)

dump(self, file, builder=<class 'csb.bio.fragments.rosetta.OutputBuilder'>)

source code

Write the library to a Rosetta fragment file.

Parameters:

file (str) - destination file name

fromsource(self, accession)

source code

Parameters:

accession (str) - source entry ID

Returns:

a tuple of all fragments, extracted from the specified source.

mark_unconfident(self, rank)

source code

Mark the specified position in the target as a low-confidence one.

Parameters:

rank (int) - position in target

read(file, top=None)
Static Method

source code

Read a standard fragment file.

Parameters:

file (str) - file name
top (int or None) - if defined, read only top fragments per start position (default=all)

Returns: RosettaFragmentMap

parsed fragment library

starting_at(self, qrank)

source code

Parameters:

qrank (int) - fragment origin (in target, rank)

Returns:

a tuple of all fragments, starting at the specified target position.

Property Details

size

Get Method:: unreachable.size(self)

sources

Get Method:: unreachable.sources(self)

start_positions

Get Method:: unreachable.start_positions(self)

unconfident_positions

Get Method:: unreachable.unconfident_positions(self)

Class RosettaFragmentMap

__init__(self, fragments, length=None) (Constructor)

__len__(self) (Length operator)

at(self, qrank)

complement(self, fragment)

dump(self, file, builder=<class 'csb.bio.fragments.rosetta.OutputBuilder'>)

fromsource(self, accession)

mark_unconfident(self, rank)

read(file, top=None) Static Method

starting_at(self, qrank)

size

sources

start_positions

unconfident_positions

init(self, fragments, length=None)
(Constructor)

len(self)
(Length operator)

read(file, top=None)
Static Method