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

handle the different way to serialize a system

__weakref__

list of weak references to the object (if defined)

TsvSystemSerializer

class macsypy.serialization.TsvSystemSerializer

Handle System serialization in tsv format

serialize(system, hit_system_tracker)

: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

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)

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

Handle potential System from unordered replicon serialization in tsv format

serialize(system, hit_system_tracker)

: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

Serialize Rejected Cluster in tsv format

__weakref__

list of weak references to the object (if defined)

serialize(candidates)

Parameters

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

TsvSpecialHitSerializer

class macsypy.serialization.TsvSpecialHitSerializer

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)

Parameters

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

TxtSystemSerializer

class macsypy.serialization.TxtSystemSerializer

Handle System serialization in text

serialize(system, hit_system_tracker)

Returns

a string representation of system readable by human

TxtLikelySystemSerializer

class macsypy.serialization.TxtLikelySystemSerializer

Handle System serialization in text

serialize(system, hit_system_tracker)

: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

Handle System serialization in text

serialize(system)

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