Class: Mspire::Ident::ProteinGroup

Inherits:
Array
  • Object
show all
Defined in:
lib/mspire/ident/protein_group.rb

Overview

represents a group of proteins, typically indistinguishable in the experiment.

Constant Summary collapse

PRIORITIZE_PROTEINS = 
lambda do |protein_group_and_peptide_hits|
  peptide_hits = protein_group_and_peptide_hits.last
  num_uniq_aaseqs = peptide_hits.map {|hit| hit.aaseq }.uniq.size
  num_uniq_aaseqs_at_z = peptide_hits.map {|hit| [hit.aaseq, hit.charge] }.uniq.size
  [num_uniq_aaseqs, num_uniq_aaseqs_at_z, peptide_hits.size]
end

Instance Attribute Summary collapse

Class Method Summary collapse

Methods inherited from Array

#in_groups

Instance Attribute Details

#peptide_hits ⇒ Object

Returns the value of attribute peptide_hits.



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# File 'lib/mspire/ident/protein_group.rb', line 8

def peptide_hits
  @peptide_hits
end

Class Method Details

.peptide_hits_to_protein_groups(peptide_hits, update_peptide_hits = false, &sort_by) ⇒ Object

greedy algorithm to map a set of peptide_hits to protein groups. each peptide hit should respond to :aaseq, :charge, :proteins if a block is given, yields a single argument: a doublet of protein_group and peptide set. It expects a metric or array to sort by for creating greedy protein groups (the greediest proteins should sort to the back of the array). if no block is given, the groups are sorted by [# uniq aaseqs, # uniq aaseq+charge, # peptide_hits] (see PRIORITIZE_PROTEINS). Sets of peptide_hits and the objects returned by peptide_hit#proteins are used as hash keys. As long as each peptide hit has a unique signature (like an id) then any object will work. If they are Struct objects, you might consider redefining the #hash method to be object_id for performance and accuracy.

returns an array of ProteinGroup objects, each set with :peptide_hits

If update_peptide_hits is true, then each peptide_hit is linked to the array of protein_groups it is associated with using :protein_groups. A symbol can also be passed in, and that method will be called instead.



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# File 'lib/mspire/ident/protein_group.rb', line 35

def self.peptide_hits_to_protein_groups(peptide_hits, update_peptide_hits=false, &sort_by)
  update_peptide_hits = 'protein_groups='.to_sym if (update_peptide_hits==true)
  sort_by ||= PRIORITIZE_PROTEINS
  # note to self: I wrote this in 2011, so I think I know what I'm doing now
  protein_to_peptides = Hash.new {|h,k| h[k] = Set.new }
  peptide_hits.each do |peptide_hit|
    peptide_hit.proteins.each do |protein|
      protein_to_peptides[protein] << peptide_hit
    end
  end
  peptides_to_protein_group = Hash.new {|h,k| h[k] = [] }
  protein_to_peptides.each do |protein, peptide_set|
    peptides_to_protein_group[peptide_set] << protein
  end
  peptides_to_protein_group.each do |pephits,ar_of_prots| 
    pg = Mspire::Ident::ProteinGroup.new(ar_of_prots)
    pg.peptide_hits = pephits
    peptides_to_protein_group[pephits] = pg
  end

  protein_group_to_peptides = peptides_to_protein_group.invert
  greedy_first = protein_group_to_peptides.sort_by(&sort_by).reverse

  accounted_for = Set.new
  # we are discarding the subsumed sets, but we could get them with
  # partition
  greedy_first.select! do |group, peptide_set|
    has_an_unaccounted_peptide = false
    peptide_set.each do |peptide_hit| 
      unless accounted_for.include?(peptide_hit) 
        has_an_unaccounted_peptide = true
        accounted_for.add(peptide_hit)
      end
    end
    group.peptide_hits = peptide_set if has_an_unaccounted_peptide
    has_an_unaccounted_peptide
  end
  if update_peptide_hits
    greedy_first.each {|pg, pephits| pephits.each {|hit| hit.send(update_peptide_hits, pg) } } 
  end
  greedy_first.map(&:first)
end