ms-in_silico 0.2.1 → 0.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/History +4 -0
- data/lib/ms/in_silico/digest.rb +1 -1
- data/lib/ms/in_silico/fragment.rb +18 -25
- metadata +2 -2
data/History
CHANGED
data/lib/ms/in_silico/digest.rb
CHANGED
@@ -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
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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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# ---
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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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#
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# :startdoc::manifest calculates a theoretical ms/ms spectrum
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#
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# Calculates the
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#
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#
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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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#
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#
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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
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@@ -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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def process(peptide)
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log :fragment, peptide
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spec = spectrum(peptide)
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@@ -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
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[masses, headers(spec)]
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end
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protected
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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.
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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
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@@ -9,7 +9,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2009-02-
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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
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