mspire-simulator 0.1.0 → 0.1.1

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bin/mspire-simulator

@@ -88,6 +88,7 @@ module MspireSimulator
     #-----------------------Clean UP----------------------------------------------
     spectra.features.each{|fe| fe.delete}
     peptides.clear
+    digester.clean
     #-----------------------------------------------------------------------------
     
     
@@ -109,6 +110,7 @@ module MspireSimulator
       if File.exists?(digester.digested_file)
         File.delete(digester.digested_file)
       end
+      digester.clean
     end
     if spectra != nil
       spectra.features.each{|fe| fe.delete}

data/lib/ms/sim_digester.rb

@@ -9,6 +9,13 @@ module MS
       @digestor = digestor
       @pH = pH
       @digested_file = ".#{Time.now.nsec.to_s}"
+      system("mkdir .m .i")
+      system("mkdir .m/A .m/R .m/N .m/D .m/C .m/E .m/Q .m/G .m/H .m/I .m/L .m/K .m/M .m/F .m/P .m/S .m/T .m/W .m/Y .m/V .m/U .m/O")
+      system("mkdir .i/A .i/R .i/N .i/D .i/C .i/E .i/Q .i/G .i/H .i/I .i/L .i/K .i/M .i/F .i/P .i/S .i/T .i/W .i/Y .i/V .i/U .i/O")
+    end
+    
+    def clean
+      system("rm -r -f .m .i")
     end
     
     def create_digested_file(file)

data/mspire-simulator.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-simulator"
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["anoyce"]
@@ -52,8 +52,7 @@ Gem::Specification.new do |s|
     "spec/peptide_spec.rb",
     "spec/progress_spec.rb",
     "spec/spec_helper.rb",
-    "spec/spectra_spec.rb",
-    "testFiles/contam/hum_keratin.fasta"
+    "spec/spectra_spec.rb"
   ]
   s.homepage = "http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html"
   s.licenses = ["MIT"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-simulator
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -217,7 +217,6 @@ files:
 - spec/progress_spec.rb
 - spec/spec_helper.rb
 - spec/spectra_spec.rb
-- testFiles/contam/hum_keratin.fasta
 homepage: http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html
 licenses:
 - MIT

data/testFiles/contam/hum_keratin.fasta

@@ -1,11 +0,0 @@
->gi|18031719|gb|AY033495.1| Homo sapiens keratin protein K6irs (KRT6) mRNA, translated
-MSRQLTHFPRGERLGFSGCSAVLSGGIGSSSASFRARVKGSASF
-GSKSLSCLGGSRSLALSAAARRGGGRLGGFVGTAFGSAGLGPKCPSVCPPGGIPQVTV
-NKSLLAPLNVEMDPEIQRVRAQEREQIKALNNKFASFIDKVRFLEQQNQVLETKWNLL
-QQLDLNNCRKNLEPIYEGYISNLQKQLEMLSGDGVRLDSELRNMQDLVEDYKKRYEVE
-INRRTAAENEFVVLKKDVDAAYMNKVELQAKVDSLTDEIKFFKCLYEGEITQIQSHIS
-DTSIVLSMDNNRDLDLDSIIAEVRAQYEEIALKSKAEAETLYQTKIQELQVTAGQHGD
-DLKLTKAEISELNRLIQRIRSEIGNVKKCADLETAIADAEQRGDCALKDARAKLDELE
-GALHQAKEELARMLREYQELVSLKLALDMEIATYRKLLESEECRMSGEYPNSVSISVI
-SSTNAGAGGAGFSMGFGASSSYSYKTAAADVKTKGSCGSELKDPLAKTSGSSCATKKA
-SR