Module: Ms::Mascot::Mgf

Defined in:
lib/ms/mascot/mgf.rb,
lib/ms/mascot/mgf/entry.rb,
lib/ms/mascot/mgf/archive.rb

Defined Under Namespace

Classes: Archive, Entry

Constant Summary collapse

VALID_LOCAL_HEADERS =

see www.matrixscience.com/help/data_file_help.html

Set.new(%w(CHARGE COMP ETAG INSTRUMENT IT_MODS PEPMASS RTINSECONDS SCANS SEQ TAG TITLE TOL TOLU))
VALID_GLOBAL_HEADERS = 
Set.new(%w(ACCESSION CHARGE CLE COM CUTOUT DB DECOY ERRORTOLERANT FORMAT FRAMES INSTRUMENT IT_MODS ITOL ITOLU MASS MODS PEP_ISOTOPE_ERROR PFA PRECURSOR QUANTITATION REPORT REPTYPE SEARCH SEG TAXONOMY TOL TOLU USER00 USER01 USER02 USER03 USER04 USER05 USER06 USER07 USER08 USER09 USER10 USER11 USER12 USEREMAIL USERNAME))

Class Method Summary collapse

Class Method Details

.foreach(file, &block) ⇒ Object

returns each entry in the mgf file, like IO.foreach



32
33
34
35
36
 
# File 'lib/ms/mascot/mgf.rb', line 32

def foreach(file, &block)
  open(file) do |ar|
    ar.each( &block )
  end
end

.open(file, &block) ⇒ Object

Opens the file and yields an array of entries (well, the array is actually an Ms::Mascot::Mgf::Archive object that acts like an array but leaves data on disk until needed)

Ms::Mascot::Mgf.open("file.mgf") do |ar|
  entry5 = ar[4]  # -> 5th entry
  entry5.pepmass  # -> peptide mass
  entry5.data     # -> array of arrays
end



22
23
24
25
26
27
28
29
 
# File 'lib/ms/mascot/mgf.rb', line 22

def open(file, &block)
  File.open(file) do |io|
    a = Archive.new(io)
    a.reindex
    block.call(a)
    a.close
  end
end

.write(outfile) {|mgf| ... } ⇒ Object

yields an Ms::Mascot::Mgf::Archive object and writes the data to outfile.

example of writing spetra to “out.mgf”:

Ms::Mascot::Mgf.write("out.mgf") do |mgf|
  # use the Query#to_mgf method:
  mgf << query.to_mgf(peptide_hit)

  # create your own entry object
  mgf << Ms::Mascot::Dat::Mgf::Entry.new(header, data)

  # push on the strings
  mgf << "BEGIN IONS"
  mgf << "TITLE=mytitle"
  # ... the rest of the info ...
  mgf << "END IONS"
end

Yields:

  • (mgf) 


56
57
58
59
60
 
# File 'lib/ms/mascot/mgf.rb', line 56

def write(outfile)
  mgf = Archive.new
  yield mgf
  mgf.close(outfile, nil, true)
end