crb-blast 0.1 → 0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c3a5d87d0431c8bdc70d1adf34e61d2c853e1364
-  data.tar.gz: 07c351d04011f795aab32983c1e69a8daaaa2407
+  metadata.gz: 4271f12aa93ccaa344fe8dbc1bcdecd1281ef7a1
+  data.tar.gz: 7222b48806f393e89c096ad50aaa92997dccbe9d
 SHA512:
-  metadata.gz: 36faeb5e2d53512661f28192212f70b080c4a98751b88d9239474279fdb5c2d03ecaa7e6f74e990a59afd19f2edebdeda596f0e613b5b2f751f4b882b84a8788
-  data.tar.gz: 276e0d706780586b6f13551aa9fa21dd1f9794fa665ae9341593aff0f6d2e12999a8e44e33918e52435726f257636146a954e7d59a11f5ac22692c9dbe644c12
+  metadata.gz: f41b2d87c4113fbb3022bfd80329c7a1224ed166c0bd3402dd15d244e1b7f69cbd6f386c6839f294a0f76e0d2adc4d7630ea59bf2dc860c06f07fedf8d4e6544
+  data.tar.gz: 2907e7327968d1edab89a3b6849e811d40e29bc8011671894708ebd656ebce1acb05e970aad0f9bfcfaddbbd2834deee9b1bb589a5e0028435c6023d1b89703d

data/bin/crb-blast

@@ -21,12 +21,12 @@ OPTIONS:
 
 EOS
   opt :query,
-      "query fasta file in nucleotide format",
+      "query fasta file",
       :required => true,
       :type => String
 
   opt :target,
-      "target fasta file as nucleotide or protein",
+      "target fasta file",
       :required => true,
       :type => String
 

data/lib/crb-blast.rb

@@ -24,11 +24,12 @@ class CRB_Blast
   attr_accessor :target_is_prot, :query_is_prot
   attr_accessor :query_results, :target_results, :working_dir
 
-  def initialize query, target, output:nil
+  def initialize query, target, output=nil
     @query = query
     @target = target
     if output.nil?
-      @working_dir = File.expand_path(File.dirname(query)) # no trailing /
+      #@working_dir = File.expand_path(File.dirname(query)) # no trailing /
+      @working_dir = "."
     else
       @working_dir = File.expand_path(output)
       mkcmd = "mkdir #{@working_dir}"
@@ -73,7 +74,7 @@ class CRB_Blast
     else
       @query_is_prot = false
     end
-    
+
     # check if the target is a nucl or prot seq
     target_file = Bio::FastaFormat.open(@target)
     count_p=0
@@ -129,7 +130,7 @@ class CRB_Blast
           cmd1 << "#{@blastp_path} "
           cmd2 << "#{@blastp_path} "
         else
-          cmd1 << "#{@tblastn_path} " 
+          cmd1 << "#{@tblastn_path} "
           cmd2 << "#{@blastx_path} "
         end
       else
@@ -174,10 +175,10 @@ class CRB_Blast
       q_count=0
       t_count=0
       if !File.exists?("#{@output1}")
-        puts "can't find #{@output1}"
+        raise RuntimeError.new("can't find #{@output1}")
       end
       if !File.exists?("#{@output2}")
-        puts "can't find #{@output2}"
+        raise RuntimeError.new("can't find #{@output2}")
       end
       if File.exists?("#{@output1}") and File.exists?("#{@output2}")
         File.open("#{@output1}").each_line do |line|
@@ -209,7 +210,7 @@ class CRB_Blast
       @reciprocals = Hash.new
       @missed = Hash.new
       @evalues = []
-      @longest=0
+      @longest = 0
       hits = 0
       @query_results.each_pair do |query_id, list_of_hits|
         list_of_hits.each_with_index do |target_hit, query_index|
@@ -321,7 +322,7 @@ class CRB_Blast
 
   def size
     hits=0
-    @reciprocals.each do |list|
+    @reciprocals.each_pair do |key, list|
       list.each do |hit|
         hits += 1
       end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: '0.1'
+  version: '0.2'
 platform: ruby
 authors:
 - Chris Boursnell
@@ -15,48 +15,48 @@ dependencies:
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
@@ -77,69 +77,68 @@ dependencies:
   name: turn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.6.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.6.7
-description: Increased sensitivity reciprocal best BLAST with automated cutoff learning
-  based on species divergence
+description: See summary
 email: cmb211@cam.ac.uk
 executables:
 - crb-blast
 extensions: []
 extra_rdoc_files: []
 files:
-- bin/crb-blast
 - lib/crb-blast.rb
 - lib/hit.rb
+- bin/crb-blast
 homepage: http://rubygems.org/gems/crb-blast
 licenses:
 - MIT
@@ -150,19 +149,19 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.0.6
 signing_key: 
 specification_version: 4
-summary: Increased sensitivity reciprocal best BLAST
+summary: Run conditional reciprocal best blast
 test_files: []
 has_rdoc: