ms-sequest 0.1.0 → 0.1.1

data/VERSION

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

data/lib/ms/sequest/params.rb

@@ -271,15 +271,17 @@ class Ms::Sequest::Params
 
   # returns the enzyme name (but no parentheses connected with the name).
   # this will likely be capitalized.
-  def enzyme
-    v = self.version
+  # the regular expression splits the name and returns the first part (or just
+  # the name if not found)
+  def enzyme(split_on=/[_\(]/)
     basic_name = 
-      if v == '3.1'
+      if self.version == '3.1'
         Bioworks31_Enzyme_Info_Array[ @opts['enzyme_number'].to_i ][0]
-      elsif v >= '3.2'
+      else    # v >= '3.2' applies to all later versions??
         @opts["enzyme_info"]
       end
-    basic_name.split('(')[0]
+    name_plus_parenthesis = basic_name.split(' ',2).first
+    name_plus_parenthesis.split(split_on,2).first
   end
 
   def max_num_internal_cleavages

data/lib/ms/sequest/srf/pepxml.rb

@@ -165,6 +165,7 @@ class Ms::Sequest::Srf
             :raw_data_type => opt[:raw_data].first,
           ) do |sample_enzyme, search_summary, spectrum_queries|
             sample_enzyme.merge!(params.sample_enzyme_hash)
+            sample_enzyme.name = opt[:enzyme] if opt[:enzyme]
             search_summary.merge!(
               :base_name=> srf.resident_dir + '/' + srf.base_name_noext,
               :search_engine => 'SEQUEST',
@@ -183,7 +184,7 @@ class Ms::Sequest::Srf
               end
 
               enzymatic_search_constraint.merge!(
-                :enzyme => params.enzyme, 
+                :enzyme => opt[:enzyme] ? opt[:enzyme] : params.enzyme, 
                 :max_num_internal_cleavages => params.max_num_internal_cleavages,
                 :min_number_termini => params.min_number_termini,
               )
@@ -269,6 +270,7 @@ module Ms::Sequest::Srf::Pepxml
       text ""
       text "major options:"
       opt :db_dir, "The dir holding the DB if different than in Srf. (pepxml requires a valid database path)", :type => :string
+      opt :enzyme, "overide the enzyme name embedded in the params file", :type => :string
       opt :mz_dir, "directory holding mz[X]ML files (defaults to the folder holding the srf file)", :type => :string
       opt :retention_times, "include retention times (requires mz-dir)"
       opt :deltacn_orig, "use original deltacn values created by SEQUEST.  By default, the top hit gets the next hit's original deltacn."

metadata

@@ -1,12 +1,8 @@
 --- !ruby/object:Gem::Specification 
 name: ms-sequest
 version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 0
-  version: 0.1.0
+  prerelease: 
+  version: 0.1.1
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-11 00:00:00 -06:00
+date: 2011-04-12 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -25,10 +21,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 0
-        - 20
         version: 0.0.20
   type: :runtime
   version_requirements: *id001
@@ -40,10 +32,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 0
-        - 17
         version: 0.0.17
   type: :runtime
   version_requirements: *id002
@@ -55,9 +43,6 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 16
         version: "1.16"
   type: :runtime
   version_requirements: *id003
@@ -69,10 +54,6 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 5
-        - 2
         version: 1.5.2
   type: :development
   version_requirements: *id004
@@ -84,10 +65,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 1
-        - 1
         version: 0.1.1
   type: :development
   version_requirements: *id005
@@ -99,8 +76,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        segments: 
-        - 0
         version: "0"
   type: :development
   version_requirements: *id006
@@ -172,21 +147,17 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      segments: 
-      - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      segments: 
-      - 0
       version: "0"
 requirements: []
 
 rubyforge_project: mspire
-rubygems_version: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc