Class: Mascot::DAT

Inherits:
Object
  • Object
show all
Defined in:
lib/mascot/dat.rb,
lib/mascot/dat/psm.rb,
lib/mascot/dat/query.rb,
lib/mascot/dat/enzyme.rb,
lib/mascot/dat/masses.rb,
lib/mascot/dat/summary.rb,
lib/mascot/dat/version.rb,
lib/mascot/dat/peptides.rb,
lib/mascot/dat/proteins.rb,
lib/mascot/dat/parameters.rb,
lib/mascot/dat/header_info.rb,
lib/mascot/dat/search_databases.rb

Overview

A parser for Mascot flat file results.

NOTE: This parser creates another file that indexes the byte position offsets of the various mime sections of a DAT file. For some reason, DAT files indexes are the line numbers within the file, making random access more difficult than it needs to be.

If you do not want this index file created, you need to pass in false to the cache_index argument

Defined Under Namespace

Classes: Enzyme, HeaderInfo, Masses, PSM, Parameters, Peptides, Proteins, Query, SearchDatabases, Summary

Constant Summary collapse

SECTIONS = 
["summary", "decoy_summary", "et_summary", "parameters",
"peptides", "decoy_peptides", "et_peptides",
"proteins", "header", "enzyme", "taxonomy", "unimod",
"quantitation", "masses", "mixture", "decoy_mixture", "index"]
VERSION = 
"0.3.1"

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dat_file_path, cache_index = true) ⇒ DAT

Returns a new instance of DAT.



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# File 'lib/mascot/dat.rb', line 35

def initialize(dat_file_path, cache_index=true)
  @dat_file = File.open(dat_file_path)
  @idx = {}
  @boundary = nil
  @boundary_string = nil
  @cache_index = cache_index
  parse_index
end

Instance Attribute Details

#boundary ⇒ Object (readonly)

Returns the value of attribute boundary.



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# File 'lib/mascot/dat.rb', line 27

def boundary
  @boundary
end

#boundary_string ⇒ Object (readonly)

Returns the value of attribute boundary_string.



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# File 'lib/mascot/dat.rb', line 28

def boundary_string
  @boundary_string
end

#dat_file ⇒ Object (readonly)

Returns the value of attribute dat_file.



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# File 'lib/mascot/dat.rb', line 29

def dat_file
  @dat_file
end

#idx ⇒ Object (readonly)

Returns the value of attribute idx.



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# File 'lib/mascot/dat.rb', line 26

def idx
  @idx
end

Class Method Details

.open(dat_file_path, cache_index = true) ⇒ Object 



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# File 'lib/mascot/dat.rb', line 44

def self.open(dat_file_path, cache_index=true)
  DAT.new(dat_file_path, cache_index)
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/mascot/dat.rb', line 48

def close
  @dat_file.close
end

#decoy_peptides(cache_psm_index = true) ⇒ Mascot::DAT::Peptides, NilClass

If the DAT file has a decoy section, puts the IO cursor at the beginning of decoy_peptide result section and returns an iterator/parser for the decoy PSM results. If no decoy section exists, it will return nil.

Parameters:

  • cache_psm_index (defaults to: true) —

    Whether to cache the positions of the PSMs. If you just want to iterate through PSMs, you do not need to cache the index.

Returns:



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# File 'lib/mascot/dat.rb', line 128

def decoy_peptides(cache_psm_index=true)
  if @idx.has_key? :decoy_peptides
    Mascot::DAT::Peptides.new(self,:decoy_peptides, cache_psm_index)
  else
    nil
  end
end

#enzyme ⇒ Array<Mascot::DAT::Enzyme>

Parse the enzyme information from the DAT file

Returns:



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# File 'lib/mascot/dat.rb', line 91

def enzyme
  @enzyme ||= Mascot::DAT::Enzyme.new(self.read_section(:enzyme))
end

#goto(key) ⇒ Object

Go to a section of the Mascot DAT file



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# File 'lib/mascot/dat.rb', line 62

def goto(key)
  if @idx.has_key?(key.to_sym)
    @dat_file.pos = @idx[key.to_sym]
  else
    raise Exception.new "Invalid DAT section \"#{key}\""
  end
end

#masses ⇒ Mascot::DAT::Masses

Parse the masses section of the DAT file

Returns:



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# File 'lib/mascot/dat.rb', line 97

def masses
  @masses ||= Mascot::DAT::Masses.new(self.read_section(:masses))
end

#parameters ⇒ Mascot::DAT::Parameters

Parses parameters from DAT file

Returns:



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# File 'lib/mascot/dat.rb', line 102

def parameters
  @params ||= Mascot::DAT::Parameters.new(self.read_section(:parameters))
end

#peptides(cache_psm_index = true) ⇒ Mascot::DAT::Peptides, NilClass

Puts the IO cursor at the beginning of peptide result section. Returns an iterator/parser for PSM results

Parameters:

  • cache_psm_index (defaults to: true) —

    Whether to cache the positions of the PSMs. If you just want to iterate through PSMs, you do not need to cache the index.

Returns:



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# File 'lib/mascot/dat.rb', line 117

def peptides(cache_psm_index=true)
  Mascot::DAT::Peptides.new(self, :peptides, cache_psm_index)
end

#proteins(cache_protein_byteoffsets = true) ⇒ Object 



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# File 'lib/mascot/dat.rb', line 137

def proteins(cache_protein_byteoffsets=true)
  Mascot::DAT::Proteins.new(self.dat_file, self.idx[:proteins], cache_protein_byteoffsets)
end

#query(n) ⇒ Mascot::DAT::Query Also known as: spectrum

Return a specific query spectrum from the DAT file

Parameters:

  • n —

    The query spectrum numerical index

Returns:



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# File 'lib/mascot/dat.rb', line 56

def query(n)
  return Mascot::DAT::Query.new(self.read_section(:"query#{n}"))
end

#read_section(key) ⇒ String

Read a section of the DAT file into memory. THIS IS NOT RECOMMENDED UNLESS YOU KNOW WHAT YOU ARE DOING.

Parameters:

  • key (String or Symbol) —

    The section name

Returns:

  • (String) —

    The section of the DAT file as a String. The section includes the MIME boundary and content type definition lines.



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# File 'lib/mascot/dat.rb', line 77

def read_section(key)
  self.goto(key.to_sym)
  # read past the initial boundary marker
  tmp = @dat_file.readline
  @dat_file.each do |l|
    break if l =~ @boundary
    tmp << l
  end
  tmp
end

#search_databases ⇒ Mascot::DAT::SearchDatabases

Parses and return search databases from DAT file

Returns:



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# File 'lib/mascot/dat.rb', line 108

def search_databases
  @search_databases ||= Mascot::DAT::SearchDatabases.new(parameters)
end