ms-in_silico 0.2.1 → 0.2.2

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data/History CHANGED
@@ -1,3 +1,7 @@
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+ == 0.2.2 / 2009-02-24
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+
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+ * updated return value of Fragment
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+
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  == 0.2.1 / 2009-02-17
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  Maintenance release with minor updates to use
@@ -5,7 +5,7 @@ module Ms
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  # Ms::InSilico::Digest::manifest digest a protein sequence into peptides
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  # Digest a protein sequence into an array of peptides.
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  #
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- # % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --+ dump --no-audit
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+ # % rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --: dump --no-audit
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  # I[14:37:55] digest MIVIGRSIVHP... to 3 peptides
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  # # date: 2008-09-15 14:37:55
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  # ---
@@ -3,32 +3,14 @@ require 'ms/in_silico/spectrum'
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  module Ms
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  module InSilico
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- # Ms::InSilico::Fragment::manifest calculates a theoretical ms/ms spectrum
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+ # :startdoc::manifest calculates a theoretical ms/ms spectrum
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  #
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- # Calculates the parent ion mass and theoretical ms/ms spectrum for a
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- # peptide sequence. Configurations allow the specification of one or
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- # more fragmentation series to include, as well as charge, and intensity.
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+ # Calculates the theoretical ms/ms spectrum for a peptide sequence.
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+ # Configurations allow the specification of one or more fragmentation series
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+ # to include, as well as charge, and intensity.
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  #
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- # % rap fragment TVQQEL --+ dump --no-audit
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- # # date: 2008-09-15 14:37:55
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- # ---
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- # ms/in_silico/fragment (:...:):
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- # - - 717.377745628191
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- # - - 102.054954926291
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- # - 132.101905118891
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- # - 201.123368842491
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- # - 261.144498215091
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- # - 329.181946353891
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- # - 389.203075726491
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- # - 457.240523865291
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- # - 517.261653237891
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- # - 586.283116961491
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- # - 616.330067154091
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- # - 699.367180941891
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- # - 717.377745628191
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- #
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- # In the output, the parent ion mass is given first, followed by an
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- # array of the sorted fragmentation data.
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+ # In the output the sorted fragmentation data is given first, followed by
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+ # a hash of header data, including the parent ion mass.
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  class Fragment < Tap::Task
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  # A block to validate a config input
@@ -48,6 +30,17 @@ module Ms
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  config :sort, true, &c.switch # sorts the data by mass
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  config :unmask, true, &c.switch # remove masked (negative) masses
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+ # Constructs a hash of header data pertinent to the spectrum.
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+ def headers(spec)
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+ {
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+ :charge => charge,
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+ :parent_ion_mass => spec.parent_ion_mass(charge),
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+ :series => series,
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+ :nterm => spec.nterm.to_s,
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+ :cterm => spec.cterm.to_s
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+ }
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+ end
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+
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  def process(peptide)
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  log :fragment, peptide
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  spec = spectrum(peptide)
@@ -58,7 +51,7 @@ module Ms
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  masses.sort! if sort
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  masses.collect! {|m| [m, intensity] } if intensity
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- [spec.parent_ion_mass(charge), masses]
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+ [masses, headers(spec)]
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  end
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  protected
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: ms-in_silico
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  version: !ruby/object:Gem::Version
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- version: 0.2.1
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+ version: 0.2.2
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  platform: ruby
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  authors:
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  - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-02-17 00:00:00 -07:00
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+ date: 2009-02-24 00:00:00 -07:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency