Class: CherrypickTask::ControlLocator

Inherits:
Object
  • Object
show all
Defined in:
app/models/cherrypick_task/control_locator.rb

Overview

A cherrypick Batch can source one or more controls from a ControlPlate For the initial destination plate in a batch these controls are distributed (pseudo)randomly across available wells. (Two controls can't occupy the same wells) Subsequent destination plates within the same batch will offset the controls by a fixed amount to ensure destination plates in a batch have different control locations. This is especially important for negative controls, as it allows plate swaps to be identified (the negative control location can be thought of as a fingerprint).

Once all well locations have been used, an new set of random locations will be generated, and the cycle will begin again.

We need to be particularly careful with the offset value, as otherwise we risk reusing wells before the full cycle has been completed. For this reason we select prime numbers that are NOT a factor of the number of available wells.

Constant Summary collapse

BETWEEN_PLATE_OFFSETS =

A cherrypick batch may contain multiple destination plates. In this case the control wells should be located at different locations on each destination. The positions on the first plate in a batch are determined randomly, and then the locations are advanced by BETWEEN_PLATE_OFFSET for each subsequent plate. This is done to avoid the risk of subsequent plates having the same negative control location, which would reduce the ability to detect plate swaps. WARNING! These needs to be a prime number (which isn't also a factor of the available well size) to avoid re-using wells prematurely. These offsets are prioritised in order. Technically any number that only shares 1 as a common factor with the available well size would work, but we limit ourself to primes to simplify validation.

[53, 59].freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(params) ⇒ ControlLocator

Note:

wells_to_leave_free was originally hardcoded for 96 well plates at 24, in order to avoid

control wells being missed in cDNA quant QC. This requirement was removed in https://github.com/sanger/sequencescape/issues/2967 however I've avoided stripping out the behaviour completely in case controls are used in other pipelines.

Parameters:

  • params (Hash) —

    A hash containing the following keys:

    • :batch_id [Integer] The id of the batch, used to generate a starting position
    • :total_wells [Integer] The total number of wells on the plate
    • :num_control_wells [Integer] The number of control wells to lay out
    • :wells_to_leave_free [Enumerable] Array or range indicating the wells to leave free from controls
    • :control_source_plate [ControlPlate] The plate to source controls from
    • :template [PlateTemplate] The template of the destination plate


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# File 'app/models/cherrypick_task/control_locator.rb', line 52

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

Instance Attribute Details

#available_positions ⇒ Object (readonly)

Returns the value of attribute available_positions.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#batch_id ⇒ Object (readonly)

Returns the value of attribute batch_id.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#control_source_plate ⇒ Object (readonly)

Returns the value of attribute control_source_plate.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#num_control_wells ⇒ Object (readonly)

Returns the value of attribute num_control_wells.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#total_wells ⇒ Object (readonly)

Returns the value of attribute total_wells.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#wells_to_leave_free ⇒ Object (readonly)

Returns the value of attribute wells_to_leave_free.



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# File 'app/models/cherrypick_task/control_locator.rb', line 32

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

Instance Method Details

#control_positions(num_plate) ⇒ Array<Integer>

Returns a list with the destination positions for the control wells distributed randomly using batch_id as seed and num_plate to increase position with plates in same batch.

Parameters:

  • num_plate (Integer) —

    The plate number within the batch

Returns:

  • (Array<Integer>) —

    The indexes of the control well positions

Raises:

  • (StandardError) 


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# File 'app/models/cherrypick_task/control_locator.rb', line 70

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#handle_incompatible_plates ⇒ Object 



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# File 'app/models/cherrypick_task/control_locator.rb', line 88

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end