Module: PhiX

Defined in:
app/models/phi_x.rb

Overview

== PhiX PhiX is a well characterized bacteriophage with a small, known, genome. It is used to provide short DNA sequences which can get added to sequencing lanes for control and calibration purposes.

== Process PhiX samples arrive on site and have tags applied as required. These may be single indexed (i7 only) or dual indexed (i5 & i7) as required. The single and dual indexed tag sets are fixed and are selected from the ‘Control Tag Group 888’ TagGroup.

Library information is filled in on the PhiXesController#show page and one or more library tubes are generated via StocksController#create and the Stock factory. These tubes are considered stocks, and get transferred to the sequencing teams.

Subsequently the sequencing team will split the contents of each LibraryTube into a number of SpikedBuffer tubes, adjusting the volume and concentration as required. This is achieved via a separate form on the PhiXesController#show page, followed by SpikedBuffersController#create and the SpikedBuffer factory.

Finally, during the processing of a SequencingPipeline the SpikedBuffer barcode is scanned in during the AddSpikedInControlTask. This adds the SpikedBuffer in as a parent of each Lane in the Batch, which in turn ensures the control can be found by batch.xml generation and Api::Messages::FlowcellIO.

== Configuration Configuration and values are stored in config/phi_x.yml tag_group_name: The name of the tag group to use tag_map_id: The default map_id for tags tag_options: Hash of available tag options, indexed by option name. Values are hashes of i5 and i7 oligos. null indicates no tag. default_tag_option: The option which will be initially selected

Defined Under Namespace

Classes: SpikedBuffer, SpikedBuffersController, Stock, StocksController

Class Method Summary collapse

Class Method Details

.configuration ⇒ Hash

Returns the configuration as defined in phi_x

Returns:

  • (Hash) —

    Configuration. See above.



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# File 'app/models/phi_x.rb', line 44

def self.configuration
  Rails.configuration.phi_x
end

.default_study_option ⇒ Object 



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# File 'app/models/phi_x.rb', line 100

def self.default_study_option
  Study.find_by(name: configuration[:default_study_option])
end

.default_tag_option ⇒ String

Returns the default tag option which will be automatically selected when generating new PhiX stocks

Returns:

  • (String) —

    The default tag option



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# File 'app/models/phi_x.rb', line 64

def self.default_tag_option
  configuration[:default_tag_option]
end

.find_tag(tag_option, tag_type) ⇒ Tag?

Returns the appropriate tag or creates it if it doesn’t exist.

Parameters:

  • tag_option (String) —

    The selected tag_option from which the tags will be selected. eg. ‘Single’

  • tag_type (:i7_oligo, :i5_oligo) —

    The tag which will be applied

Returns:

  • (Tag, nil) —

    The tag to apply, or nil if it is to be untagged



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# File 'app/models/phi_x.rb', line 123

def self.find_tag(tag_option, tag_type)
  oligo = tag_options.dig(tag_option.to_sym, tag_type)
  return nil if oligo.nil?

  tag_group.tags.create_with(map_id: configuration[:tag_map_id]).find_or_create_by!(oligo:)
end

.sample ⇒ Sample

Returns the sample the represents PhiX, creates it if it doesn’t exist

Returns:



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# File 'app/models/phi_x.rb', line 84

def self.sample
  Sample.find_or_create_by!(name: 'phiX_for_spiked_buffers')
end

.spiked_buffer_purpose ⇒ Tube::Purpose

Returns the purpose used to generate new PhiX SpikedBuffers creates it if it doesn’t exist

Returns:



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# File 'app/models/phi_x.rb', line 78

def self.spiked_buffer_purpose
  Tube::Purpose.create_with(target_type: 'SpikedBuffer').find_or_create_by(name: 'PhiX Spiked Buffer')
end

.stock_purpose ⇒ Tube::Purpose

Returns the purpose used to generate new PhiX Stocks creates it if it doesn’t exist

Returns:



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# File 'app/models/phi_x.rb', line 71

def self.stock_purpose
  Tube::Purpose.create_with(target_type: 'LibraryTube').find_or_create_by(name: 'PhiX Stock')
end

.studies ⇒ Study::ActiveRecord_Relation

Returns the studies that can be used to register PhiX

Returns:

  • (Study::ActiveRecord_Relation) 


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# File 'app/models/phi_x.rb', line 96

def self.studies
  Study.where(name: configuration[:studies])
end

.tag_group ⇒ TagGroup

Returns the tag group for PhiX tags or creates it if it doesn’t exist

Returns:

  • (TagGroup) —

    The TagGroup for PhiX tags



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# File 'app/models/phi_x.rb', line 90

def self.tag_group
  TagGroup.find_or_create_by!(name: configuration[:tag_group_name])
end

.tag_option_for(i7_oligo:, i5_oligo:) ⇒ String

Performs a lookup of the tag option matching the given oligo pair. If no option can be found returns: UNKOWN i7:i7_olgo i5:i5_oligo

Parameters:

  • i7_oligo (String) —

    The i7 (tag) oligo sequence

  • i5_oligo (String) —

    The i5 (tag2) oligo sequence

Returns:

  • (String) —

    The named tag option.



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# File 'app/models/phi_x.rb', line 112

def self.tag_option_for(i7_oligo:, i5_oligo:)
  tag_options.deep_symbolize_keys.key(i7_oligo:, i5_oligo:)&.to_s ||
    "UNKNOWN i7:#{i7_oligo || '-'} i5:#{i5_oligo || '-'}"
end

.tag_option_names ⇒ Array

Returns the names of valid tag options for creation of PhiX libraries.

Returns:

  • (Array) —

    Valid tag options



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# File 'app/models/phi_x.rb', line 57

def self.tag_option_names
  tag_options.keys.map(&:to_s)
end

.tag_options ⇒ Hash

Returns the tag_options configured.

Returns:

  • (Hash) —

    Hash of available tag options, indexed by option name. Values are hashes of i5 and i7 oligos. null indicates no tag.



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# File 'app/models/phi_x.rb', line 51

def self.tag_options
  configuration[:tag_options]
end