crb-blast 0.5.0 → 0.6.3.b

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f89145eb1bb4b80cc97d2e31ea2c3ea0607c0e97
-  data.tar.gz: 7b4e48dc974fbec26342d47ddb5080d4b51b2aee
+  metadata.gz: bf6e729c7f540f1aa50dbc880c9d605325dc6e07
+  data.tar.gz: db98e708ebb7412c63753038d6a32b62d68972d3
 SHA512:
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-  data.tar.gz: 08676fab1f78f3e2db3196283c1ff6f467f3af5d0d9112901f5c8b959639a4e6b6035d2673abd258ab77219821a69e0e2f51aaffd1ad4c119ccb931b095b96d7
+  metadata.gz: 26a19961c0f8c6c702b339933a3a807eddc44ff14c10bd2824918cab6c2b8f22fa244eddbe8c70f4053613e3cd16fb16ec17692c2398d998bb83b10da2b2de89
+  data.tar.gz: 19e35ef6a261214882c42200ecb0800d7eb86d39d9cb6e58165d5c07bc630e067abfade70d4b4e3eca9052357ff4fb91a591075b7f16c0d960245ab3fa82e39e

data/crb-blast.gemspec

@@ -4,7 +4,7 @@ require File.expand_path('../lib/crb-blast/version', __FILE__)
 Gem::Specification.new do |gem|
   gem.name        = 'crb-blast'
   gem.version     = CRB_Blast::VERSION::STRING.dup
-  gem.date        = '2014-12-07'
+  gem.date        = '2015-05-19'
   gem.summary     = "Run conditional reciprocal best blast"
   gem.description = "See summary"
   gem.authors     = ["Chris Boursnell", "Richard Smith-Unna"]
@@ -19,7 +19,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'fixwhich', '~> 1.0', '>= 1.0.2'
   gem.add_dependency 'threach', '~> 0.2', '>= 0.2.0'
-  gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.1'
+  gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.3'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
   gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'

data/lib/crb-blast/crb-blast.rb

@@ -228,6 +228,12 @@ module CRB_Blast
           cmd1 = "#{bin1} -query #{thread} -db #{@working_dir}/#{@target_name} "
           cmd1 << " -out #{thread}.blast -evalue #{evalue} "
           cmd1 << " -outfmt \"6 std qlen slen\" "
+          if bin1=~/blastn/
+            cmd1 << " -dust no "
+          elsif bin1=~/blastx/ or bin1=~/blastp/ or bin1=~/tblastn/
+            cmd1 << " -seg no "
+          end
+          cmd1 << " -soft_masking false "
           cmd1 << " -max_target_seqs 50 "
           cmd1 << " -num_threads 1"
           if !File.exists?("#{thread}.blast")
@@ -357,14 +363,14 @@ module CRB_Blast
         if File.exists?("#{@output1}") and File.exists?("#{@output2}")
           File.open("#{@output1}").each_line do |line|
             cols = line.chomp.split("\t")
-            hit = Hit.new(cols)
+            hit = Hit.new(cols, @query_is_prot, @target_is_prot)
             @query_results[hit.query] = [] if !@query_results.has_key?(hit.query)
             @query_results[hit.query] << hit
             q_count += 1
           end
           File.open("#{@output2}").each_line do |line|
             cols = line.chomp.split("\t")
-            hit = Hit.new(cols)
+            hit = Hit.new(cols, @target_is_prot, @query_is_prot)
             @target_results[hit.query] = [] if !@target_results.has_key?(hit.query)
             @target_results[hit.query] << hit
             t_count += 1
@@ -396,9 +402,7 @@ module CRB_Blast
                   e = target_hit.evalue.to_f
                   e = 1e-200 if e==0
                   e = -Math.log10(e)
-                  if !@reciprocals.key?(query_id)
-                    @reciprocals[query_id] = []
-                  end
+                  @reciprocals[query_id] ||= []
                   @reciprocals[query_id] << target_hit
                   hits += 1
                   @longest = target_hit.alnlen  if target_hit.alnlen > @longest
@@ -461,11 +465,11 @@ module CRB_Blast
               if e >= fitting[l]
                 if !@reciprocals.key?(id)
                   @reciprocals[id] = []
-                  found=false
+                  found = false
                   @reciprocals[id].each do |existing_hit|
                     if existing_hit.query == hit.query &&
                       existing_hit.target == hit.target
-                     found=true
+                     found = true
                     end
                   end
                   if !found
@@ -488,6 +492,22 @@ module CRB_Blast
       @target_results = nil
     end
 
+    # delete blast database files
+    def tidy_up
+      Dir["*nin"].each do |file|
+        File.delete(file)
+      end
+      Dir["*nhr"].each do |file|
+        File.delete(file)
+      end
+      Dir["*nsq"].each do |file|
+        File.delete(file)
+      end
+      Dir["*blast"].each do |file|
+        File.delete(file)
+      end
+    end
+
     def run evalue=1e-5, threads=1, split=true
       makedb
       run_blast evalue, threads, split

data/lib/crb-blast/hit.rb

@@ -4,10 +4,10 @@ module CRB_Blast
     # Fields: query id, subject id, % identity, alignment length, mismatches,
     # gap opens, q. start, q. end, s. start, s. end, evalue, bit score
     attr_accessor :query, :target, :id, :alnlen, :mismatches, :gaps, :qstart,
-    :qend, :tstart, :tend, :evalue, :bitscore, :qlen, :tlen
+    :qend, :tstart, :tend, :evalue, :bitscore, :qlen, :tlen, :qprot, :tprot
 
-    def initialize(list)
-      raise(RuntimeError, "unexpected number of columns") unless list.length==14
+    def initialize(list, qprot, tprot)
+      raise(RuntimeError, "unexpected number of columns") if list.length < 14
       @query      = list[0].split(/[\|\ ]/).first
       @target     = list[1].split(/[\|\ ]/).first
       @id         = list[2]
@@ -22,11 +22,13 @@ module CRB_Blast
       @bitscore   = list[11].to_f
       @qlen       = list[12].to_f
       @tlen       = list[13].to_f
+      @qprot      = qprot # bool
+      @tprot      = tprot # bool
     end
 
     def to_s
       s = "#{@query}\t#{@target}\t#{@id}\t#{@alnlen}\t#{@evalue}\t#{@bitscore}\t"
-      s << "#{@qstart}..#{@qend}\t#{@tstart}..#{@tend}"
+      s << "#{@qstart}..#{@qend}\t#{@tstart}..#{@tend}\t#{@qlen}\t#{@tlen}"
       return s
     end
   end

data/lib/crb-blast/version.rb

@@ -2,11 +2,11 @@ module CRB_Blast
 
   module VERSION
     MAJOR = 0
-    MINOR = 5
-    PATCH = 0
-    BUILD = nil
+    MINOR = 6
+    PATCH = 3
+    BUILD = 'b'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end
 
-end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.6.3.b
 platform: ruby
 authors:
 - Chris Boursnell
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-07 00:00:00.000000000 Z
+date: 2015-05-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -94,7 +94,7 @@ dependencies:
         version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: 1.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -104,7 +104,7 @@ dependencies:
         version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: 1.0.3
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -242,9 +242,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.2.2