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¶
TsvSystemSerializer¶
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class
macsypy.serialization.
TsvSystemSerializer
[source]¶ Handle System serialization in tsv format
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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 hitin 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
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TsvSolutionSerializer¶
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class
macsypy.serialization.
TsvSolutionSerializer
[source]¶ Handle Solution (list of Systems) serialization in tsv format
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__weakref__
¶ list of weak references to the object (if defined)
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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.- solution (list of
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TsvLikelySystemSerializer¶
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class
macsypy.serialization.
TsvLikelySystemSerializer
[source]¶ Handle potential System from unordered replicon serialization in tsv format
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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 - :param
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TsvRejectedCandidatesSerializer¶
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class
macsypy.serialization.
TsvRejectedCandidatesSerializer
[source]¶ Serialize Rejected Cluster in tsv format
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__weakref__
¶ list of weak references to the object (if defined)
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serialize
(candidates)[source]¶ Parameters: candidates ([ macsypy.system.RejectedCandidate
object, …]) – list of rejected candidates to serialize
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TsvSpecialHitSerializer¶
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class
macsypy.serialization.
TsvSpecialHitSerializer
[source]¶ Serialize special hits:
macsypy.hit.Loner
andmacsypy.hit.MultiSystem
in tsv format-
__weakref__
¶ list of weak references to the object (if defined)
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serialize
(best_hits)[source]¶ Parameters: best_hits (sequence of macsypy.hit.Loner
ormacsypy.hit.MultiSystem
objects) – the special hits to serialized
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TxtSystemSerializer¶
TxtLikelySystemSerializer¶
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class
macsypy.serialization.
TxtLikelySystemSerializer
[source]¶ Handle System serialization in text
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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 - :param
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TxtUnikelySystemSerializer¶
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class
macsypy.serialization.
TxtUnikelySystemSerializer
[source]¶ Handle System serialization in text
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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
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