Class: Ms::Mascot::Dat::Peptides

Inherits:
Section
  • Object
show all
Includes:
Utils
Defined in:
lib/ms/mascot/dat/peptides.rb

Overview

Peptides represent peptide identification information in a dat file.

Content-Type: application/x-Mascot; name="peptides"

q1_p1=-1
q2_p1=0,499.300598,-0.051862,2,LAVPT,10,0000000,3.87,0001002000000000000,0,0;"Y1319_MYCTU":0:531:535:1,"Y1353_MYCBO":0:531:535:1
q2_p1_terms=R,-:R,-
q2_p2=0,499.300598,-0.051862,2,LAVTP,10,0000000,3.87,0001002000000000000,0,0;"RLPA_RICCN":0:316:320:1
q2_p2_terms=K,-
q2_p3=0,499.336990,-0.088254,2,LAVVV,10,0000000,3.87,0001002000000000000,0,0;"DYNA_NEUCR":0:1296:1300:1
q2_p3_terms=R,-

Peptides is a standard Section and simply defines methods for convenient access. See Section for parsing details.

Interpretation

Deciphering the peptide information requires some cross-referencing with online results. Note that a single query can match multiple peptides.

qN_pM=-1                         # no matches
qN_pM=peptide;protein_maps       # query N peptide hit M
qN_pM_terms=A,B:C,D              # n and c-termini residues for each protein match

See the Peptide and ProteinMap structures for interpretation of the specific query data.

Defined Under Namespace

Modules: Utils Classes: PeptideHit, ProteinMap

Constant Summary collapse

PeptideHitFloatIndicies =

Indicies of PeptideHit terms that will be cast to floats.

[1,2,7]
PeptideHitIntIndicies =

Indicies of PeptideHit terms that will be cast to integers.

[0,3,5,9,10]
ProteinMapIntIndicies =

Indicies of ProteinMap terms that will be cast to integers.

[1,2,3,4]

Constants inherited from Section

Section::CONTENT_TYPE_REGEXP, Section::TO_S_FORMAT

Instance Attribute Summary

Attributes inherited from Section

#dat, #data, #section_name

Instance Method Summary collapse

Methods included from Utils

parse_peptide_hit

Methods inherited from Section

parse, section_name, #to_s

Constructor Details

#initialize(data = {}, section_name = self.class.section_name, dat = nil) ⇒ Peptides

Returns a new instance of Peptides.



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# File 'lib/ms/mascot/dat/peptides.rb', line 165

def initialize(data={}, section_name=self.class.section_name, dat=nil)
  super(data, section_name, dat)
  @queries = []
end

Instance Method Details

#peptide_hit(query, hit = 1) ⇒ Object

Returns the PeptideHit at the query and hit index, or nil if no such hit exists.



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# File 'lib/ms/mascot/dat/peptides.rb', line 194

def peptide_hit(query, hit=1)
  key = "q#{query}_p#{hit}"
  return nil unless data.has_key?(key)
  
  hits = @queries[query] ||= []
  if existing_hit = hits[hit]
    return existing_hit
  end
  
  if parsed_hit = parse_peptide_hit(data[key], data["#{key}_terms"])
    parsed_hit.query_num = query
    parsed_hit.hit_num = hit
    hits[hit] = parsed_hit
    return parsed_hit
  end
  
  nil
end

#peptide_hits(query) ⇒ Object

Returns an array of PeptideHits for the specified query, or nil if no such query exists.



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# File 'lib/ms/mascot/dat/peptides.rb', line 186

def peptide_hits(query)
  hit = 1
  hit += 1 while peptide_hit(query, hit)
  @queries[query]
end

#queries(resolve = true) ⇒ Object

An array of peptides hits per query. Specify resolve=false to return the currently parsed queries.

Note that the queries array is indexed the same as in Mascot, ie the PeptideHit for q1_p1 is located at queries[1], meaning there is always an empty cell at queries.



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# File 'lib/ms/mascot/dat/peptides.rb', line 176

def queries(resolve=true)
  return @queries unless resolve
  
  query = 1
  query += 1 while peptide_hits(query)
  @queries
end