scbi_blast 0.0.30 → 0.0.31

data/lib/scbi_blast/dust_masker.rb

@@ -1,103 +1,118 @@
-
+# Copyright (c) 2010 Dario Guerrero & Almudena Bocinos
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# 'Software'), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+# DustQuery class
 class DustQuery
-  
+
   attr_accessor :query_id,:dust
-  
+
   def initialize(query_id)
     @dust=[]
     @query_id = query_id
   end
-  
+
   def push(interval)
     @dust.push interval
   end
-  
+
   def inspect
     res= "Query #{query_id}:"
     @dust.each do |d|
       res += " from #{d[0]} to #{d[1]}"
     end
   end
-  
+
 end
 
+# DustMasker launcher class
 class DustMasker
 
-def initialize(extra_params = '')
+  # initializator
+  def initialize(extra_params = '')
 
-		@format = 'interval'
+    @format = 'interval'
     @extra_params=extra_params
-   
-end
 
-def get_cmd(extra_params = '')
+  end
+
+  # returns command to be executed
+  def get_cmd(extra_params = '')
 
     cmd = 'dustmasker '+@extra_params + '-outfmt '+ @format + ' 2>/dev/null'
     return cmd
 
-end
+  end
 
-def do_dust(seq_fasta)
+  # do the processing with dustmasker to a set of sequences in fasta stored in a string
+  def do_dust(seq_fasta)
     intervals=[]
-    
+
     if !seq_fasta.nil? && !seq_fasta.empty?
-      
+
       if seq_fasta.is_a?(Array)
         seq_fasta=seq_fasta.join("\n")
       end
-      
+
       cmd = get_cmd(@extra_params)
       if !seq_fasta.index('>')
         raise "Data passed to dust must be in fasta format"
       end
 
       # puts seq_fasta
-  		res=''
+      res=''
 
-      # Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se  encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando sólo los 20 primeros nt.
+      # Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se  encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
       IO.popen(cmd,'w+') {|blast|
-         blast.sync = true
-         # blast.write(">seq\n")
-         blast.write(seq_fasta)
-         blast.close_write
-         res = blast.readlines
-         blast.close_read
+        blast.sync = true
+        # blast.write(">seq\n")
+        blast.write(seq_fasta)
+        blast.close_write
+        res = blast.readlines
+        blast.close_read
       }
-      
+
       if !$?.exitstatus.nil? && $?.exitstatus>0
         raise "Error while doing #{cmd} to seq: #{seq_fasta}"
       end
-      # puts cmd    
-      # puts $?.class
-      # puts res
-      #parse results
-    
-      # >seq
-      # 3 - 346
-      # 354 - 683
-      # .
-    
+
 
       res.each do |line|
         # puts "LINEA:" + line
-        if line =~ /^>(.*)$/ 
+        if line =~ /^>(.*)$/
           intervals.push DustQuery.new($1)
         elsif line =~ /^(\d+)\s\-\s(\d+)/
           # puts "Algo #{$1}, #{$2}"
           intervals.last.push [$1.to_i,$2.to_i]
         end
-      
+
       end
     end
-    
-    return intervals
 
-end
+    return intervals
 
-def close
-	
-end
+  end
 
-end
+  def close
 
+  end
 
+end

data/lib/scbi_blast.rb

@@ -1,3 +1,25 @@
+# Copyright (c) 2010 Dario Guerrero & Almudena Bocinos
+# 
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# 'Software'), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+# 
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+# 
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
 $: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))		
 
 require 'batch_blast'
@@ -9,7 +31,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-  VERSION = '0.0.30'
+  VERSION = '0.0.31'
 end
 
 

metadata

@@ -2,7 +2,7 @@
 name: scbi_blast
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.30
+  version: 0.0.31
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-26 00:00:00 Z
+date: 2011-04-28 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -23,7 +23,9 @@ dependencies:
         version: 2.8.0
   type: :development
   version_requirements: *id001
-description: FIX (describe your package)
+description: |-
+  scbi_blast is a ruby gem to handle blast+ executions without the need of temporary files, 
+  it has been developed at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero.
 email: 
 - dariogf@gmail.com, alkoke@gmail.com
 executables: []
@@ -56,7 +58,7 @@ files:
 - lib/scbi_blast/blast_simplexml_result.rb
 - lib/scbi_blast/batch_blast.rb
 - lib/scbi_blast/dust_masker.rb
-homepage: http://github.com/#{github_username}/#{project_name}
+homepage: http://www.scbi.uma.es/downloads
 licenses: []
 
 post_install_message: PostInstall.txt
@@ -83,7 +85,7 @@ rubyforge_project: scbi_blast
 rubygems_version: 1.7.2
 signing_key: 
 specification_version: 3
-summary: FIX (describe your package)
+summary: scbi_blast is a ruby gem to handle blast+ executions without the need of temporary files,  it has been developed at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero.
 test_files: 
 - test/test_helper.rb
 - test/test_scbi_blast.rb