alphabase.protein.protein_level_decoy#

Protein reverse decoy defined in ProteinReverseDecoy. This class is also registered in decoy_lib_provider.

Classes:

ProteinReverseDecoy(target_lib)

class alphabase.protein.protein_level_decoy.ProteinReverseDecoy(target_lib: SpecLibFasta)[source][source]#

Bases: SpecLibDecoy

Methods:

__init__(target_lib)

param target_lib:

Target library to decoy.

append_to_target_lib()

A decoy method should define how to append itself to target_lib.

decoy_sequence()

Generate decoy sequences from self.target_lib.
__init__(target_lib: SpecLibFasta)[source][source]#
Parameters:

  • target_lib (SpecLibBase) – Target library to decoy.

  • fix_C_term (bool, optional) – If fix C-term AA when decoy. Defaults to True.

target_lib#

same as ‘target_lib’ in Args.

Type:

SpecLibBase

append_to_target_lib()[source][source]#

A decoy method should define how to append itself to target_lib. Sub-classes should override this method when necessary.

decoy_sequence()[source][source]#

Generate decoy sequences from self.target_lib. Sub-classes should override the _decoy_seq method when necessary.

Parameters:

  • multiprocessing (bool, optional) – If true use multiprocessing. Defaults to True.

  • mp_batch_size (int, optional) – Batch size for multiprocessing. Defaults to 10000.

  • mp_process_num (int, optional) – Number of processes for multiprocessing. Defaults to 8.