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

source code

                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)