Module: Mspire::Ident

Defined in:
lib/mspire/ident.rb,
lib/mspire/ident/pepxml.rb,
lib/mspire/ident/search.rb,
lib/mspire/ident/peptide.rb,
lib/mspire/ident/protein.rb,
lib/mspire/ident/peptide/db.rb,
lib/mspire/ident/peptide_hit.rb,
lib/mspire/ident/protein_group.rb,
lib/mspire/ident/pepxml/parameters.rb,
lib/mspire/ident/pepxml/search_hit.rb,
lib/mspire/ident/peptide_hit/qvalue.rb,
lib/mspire/ident/pepxml/modifications.rb,
lib/mspire/ident/pepxml/sample_enzyme.rb,
lib/mspire/ident/pepxml/search_result.rb,
lib/mspire/ident/pepxml/search_summary.rb,
lib/mspire/ident/pepxml/spectrum_query.rb,
lib/mspire/ident/pepxml/search_database.rb,
lib/mspire/ident/pepxml/msms_run_summary.rb,
lib/mspire/ident/pepxml/msms_pipeline_analysis.rb,
lib/mspire/ident/pepxml/search_hit/modification_info.rb

Overview

An Mspire::Ident::ProteinGroup is an array of proteins that responds to :peptide_hits. All protein level identifications should be stored in a proteingroup object.

An Mspire::Ident::Protein is an object representing a protein (:id, :sequence, :description). Note, it is not a protein hit (use a ProteinGroup)

An Mspire::Ident::PeptideHit is an object representing a match between an amino acid sequence and a spectrum.

Typical usage:

require 'mspire/ident'

hit1 = PeptideHit.new(:id => 1, :aaseq => 'PEPTIDE', :search =>
Mspire::Ident::Search.new, etc...)
peptide_hits = [hit1, hit2, ...]

protein_groups = Mspire::Ident::ProteinGroup.peptide_hits_to_protein_groups(peptide_hits)
protein_groups.first.peptide_hits  # => the peptide hits in that group

Defined Under Namespace

Modules: Peptide, PeptideHitLike, ProteinLike, SearchGroup, SearchLike Classes: PeptideHit, Pepxml, Protein, ProteinGroup, Search

Class Method Summary collapse

Class Method Details

.filetype(file) ⇒ Object

returns the filetype (if possible)



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# File 'lib/mspire/ident.rb', line 31

def self.filetype(file)
  if file =~ /\.srf$/i
    :srf
  end
end