serialization

This module is a technical module where we can find the different way to serialize the results:

  • the Systems found
  • The best solutions (best combination of systems)
  • The rejected clusters
class macsypy.serialization.SystemSerializer[source]

handle the different way to serialize a system

__weakref__

list of weak references to the object (if defined)

class macsypy.serialization.TxtSystemSerializer[source]

Handle System serialization in text

serialize(system, hit_system_tracker)[source]
Returns:a string representation of system readable by human
class macsypy.serialization.TsvSystemSerializer[source]

Handle System serialization in tsv format

serialize(system, hit_system_tracker)[source]
Returns:a serialisation of this system in tabulated separated value format each line represent a hit and have the following structure:
replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_loci\tlocus_num\tsys_wholeness\tsys_score \tsys_occ\thit_gene_ref.alternate_of\thit_status\thit_seq_len\thit_i_eval\thit_score\thit_profile_cov \thit_seq_cov\tit_begin_match\thit_end_match
Return type:str
class macsypy.serialization.TsvSolutionSerializer[source]

Handle Solution (list of Systems) serialization in tsv format

__init__()[source]

Constructor

__weakref__

list of weak references to the object (if defined)

serialize(solution, sol_id, hit_system_tracker)[source]
Parameters:
Returns:

a serialisation of this solution (a list of systems) in tabulated separated value format each line represent a hit and have the same structure as system serialization macsypy.serialization.TsvSystemSerializer.serialize() but with an extra column sol_id which is a technical id to identified the different solutions.