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mascot dat file parser for the mspire library
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lib/mspire/mascot
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mspire-mascot-dat.gemspec

README.md

mspire-mascot-dat

Access mascot search engine .dat results file.

  • Simple interface
  • Lazy reading from IO object
  • Object access of key data types
  • Data casts where appropriate

Pull requests (or requests for features) gladly accepted.

API of latest version

Synposis

A Dat object reads information off an open IO object as lazily as possible. The sections can be accessed like a hash.

require 'mspire-mascot-dat'

Mspire::Mascot::Dat.open(file.dat) do |dat|
  dat.keys # (or dat.sections) => [:parameters, :masses, ...]

  dat[:peptides].each do |peptide|
    # or:    dat.each_peptide {|peptide| ... }
    # data is properly cast
    peptide.delta             # => a Float
    peptide.missed_cleavages  # => an Integer
  end

  dat[:queries].each do |query|
    query.title   # => a String (unescaped)
  end

  dat[:proteins].each do |protein|
    protein.accession
  end

  # or random query access
  dat.query(22)   # returns query #22

  # sections with uppercase params are typically accessed by string
  params = dat[:parameters]
  params['CHARGE'] # => an Integer

  # sections with lowercase params are accessed by symbol
  header = dat[:header]
  header[:sequences] # => an Integer

  # sections that aren't normal key/value pairs returned as a String
  dat[:unimod]   # => a String containing lots of XML
  dat[:enzyme]   # => a String with enzyme data
end

Note that no support is given for accessing the 'summary' sections because they are often incomplete for large files anyway and the information can all be found by accessing the

Enumerable information

Sections with enumerable objects may be accessed as each_ or with Dat#[], which returns an enumerable. So, these are equivalent:

dat.each_peptide {|pep| ... }
dat[:peptides].each {|pep| ... }

# these also are equivalent (return an enumerator)
enumerator = dat.each_peptide
enumerator = dat[:peptides]

Enumerators for some objects will have additional parameters that may be passed in (to either method style). For instance, the user may retrieve the top n peptide hits:

dat.each_peptide(1) {|peptide| ... } # only top peptide hits

Queries

In a dat file, each query is its own section, but this makes them fairly awkward to access. We treat them as if they were grouped into a single section.

dat[:queries].each do |query|
  # hash or method access
  query[:charge] # => a positive or negative Integer
  query.charge 
  query.Ions1 # or query.peaks
end

But they can also be accessed by query number:

dat.query(23)  # return query23

Decoys

Decoy peptides may be accessed a few different ways, all of which are equivalent:

dat.each_peptide(false)    {|peptide| ... }
dat[:peptides, false].each {|peptide| ... }
dat.each_decoy_peptide     {|peptide| ... }
dat[:decoy_peptides].each  {|peptide| ... }

Further Info

See the specs for additonal examples.

Also, see Mascot's "Installation & Setup Manual" for detailed information about the .dat format itself (can be accessed from the mascot main page of whichever mascot you are using).

Copyright

MIT. See LICENSE.txt

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