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 candidates

SystemSerializer¶

class macsypy.serialization.SystemSerializer[source]¶

handle the different way to serialize a system

__weakref__¶: list of weak references to the object (if defined)

TsvSystemSerializer¶

class macsypy.serialization.TsvSystemSerializer[source]¶

Handle System serialization in tsv format

serialize(system, hit_system_tracker)[source]¶

:param macsypy.system.System system: The system to serialize. :param hit_system_tracker: The hit_system_tracker which allow to know for each hit

in which system it is implied.

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\tcounterpart\tused_in_systems

Return type:	str

TsvSolutionSerializer¶

class macsypy.serialization.TsvSolutionSerializer[source]¶

Handle Solution (list of Systems) serialization in tsv format

__weakref__¶: list of weak references to the object (if defined)

serialize(solution, sol_id, hit_system_tracker)[source]¶

Parameters:	solution (list of `macsypy.system.System` object) – the solution to serialize sol_id (int) – the solution identifier hit_system_tracker (`macsypy.system.HitSystemTracker` object) –
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.

TsvLikelySystemSerializer¶

class macsypy.serialization.TsvLikelySystemSerializer[source]¶

Handle potential System from unordered replicon serialization in tsv format

serialize(system, hit_system_tracker)[source]¶

:param macsypy.system.LikelySystem system: The likely system to serialize.: Use only for unordered db-type

Parameters:	hit_system_tracker (`macsypy.system.HitSystemTracker` object) – The hit_system_tracker which allow to know for each hit in which system it is implied.
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_wholeness
\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\t$used_in_systems

Return type:	str

TsvRejectedCandidatesSerializer¶

class macsypy.serialization.TsvRejectedCandidatesSerializer[source]¶

Serialize Rejected Cluster in tsv format

__weakref__¶: list of weak references to the object (if defined)

serialize(candidates)[source]¶

Parameters:	candidates ([ `macsypy.system.RejectedCandidate` object, …]) – list of rejected candidates to serialize

TsvSpecialHitSerializer¶

class macsypy.serialization.TsvSpecialHitSerializer[source]¶

Serialize special hits: macsypy.hit.Loner and macsypy.hit.MultiSystem in tsv format

__weakref__¶: list of weak references to the object (if defined)

serialize(best_hits)[source]¶

Parameters:	best_hits (sequence of `macsypy.hit.Loner` or `macsypy.hit.MultiSystem` objects) – the special hits to serialized

TxtSystemSerializer¶

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

TxtLikelySystemSerializer¶

class macsypy.serialization.TxtLikelySystemSerializer[source]¶

Handle System serialization in text

serialize(system, hit_system_tracker)[source]¶

:param macsypy.system.LikelySystem system: The likely system to serialize.: Use only for unordered db-type

Parameters:	hit_system_tracker (`macsypy.system.HitSystemTracker` object) – The hit_system_tracker which allow to know for each hit in which system it is implied.
Returns:	a string representation of system readable by human

TxtUnikelySystemSerializer¶

class macsypy.serialization.TxtUnikelySystemSerializer[source]¶

Handle System serialization in text

serialize(system)[source]¶

Parameters:	system (`macsypy.system.UnlikelySystem` object) – The unlikely system to serialize. (used only if db-type is “unordered_replicon”)
Returns:	a string representation of system readable by human