ms-in_silico 0.2.3 → 0.3.0
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- data/History +4 -0
- data/lib/ms/in_silico/digest.rb +2 -2
- data/lib/ms/in_silico/fragment.rb +8 -5
- metadata +14 -4
data/History
CHANGED
data/lib/ms/in_silico/digest.rb
CHANGED
@@ -1,12 +1,12 @@
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require 'tap/task'
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require 'ms/in_silico/digester'
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module Ms
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module InSilico
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#
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# :startdoc::task 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 --:i dump
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# I[14:37:55] digest MIVIGRSIVHP... to 3 peptides
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# MIVIGR
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# SIVHPYITNEYEPFAAEK
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# QQILSIMAG
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@@ -1,9 +1,10 @@
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require 'tap/task'
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require 'ms/in_silico/spectrum'
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module Ms
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module InSilico
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# :startdoc::
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# :startdoc::task calculates a theoretical ms/ms spectrum
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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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@@ -13,18 +14,20 @@ module Ms
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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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# is an EmpericalFormula.
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MOLECULE = lambda do |value|
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empirical_formula_block = lambda do |value|
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case value
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when Molecules::EmpiricalFormula then value
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else Molecules::EmpiricalFormula.parse(value)
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end
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end
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# A block to validate a config input
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# is an EmpericalFormula.
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MOLECULE = empirical_formula_block
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config :series, ['y', 'b'], &c.list # a list of the series to include
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config :charge, 1, &c.integer # the charge for the parent ion
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config :intensity, nil, &c.
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config :intensity, nil, &c.numeric_or_nil # a uniform intensity value
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config :nterm, 'H', &MOLECULE # the n-terminal modification
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config :cterm, 'OH', &MOLECULE # the c-terminal modification
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config :sort, true, &c.switch # sorts the data by mass
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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.
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version: 0.3.0
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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-
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date: 2009-05-25 00:00:00 -06:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.17.0
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version:
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- !ruby/object:Gem::Dependency
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name: tap-test
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type: :development
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version_requirement:
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.1.0
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version:
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- !ruby/object:Gem::Dependency
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name: molecules
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.2.0
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version:
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description:
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email: simon.a.chiang@gmail.com
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