scbi_blast 0.0.34 → 0.0.37

data/History.txt

@@ -1,3 +1,15 @@
+=== 0.0.37 2012-11-28
+
+Fixed empty seqs
+
+=== 0.0.36 2012-11-28
+
+Protect against empty seqs and results
+
+=== 0.0.35 2012-11-28
+
+Protect against empty seqs
+
 === 0.0.34 2012-04-30
 
 Added streamed XML parser to reduce memory usage with xml tree

data/lib/scbi_blast.rb

@@ -33,7 +33,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-   VERSION = '0.0.34'
+   VERSION = '0.0.37'
 end
 
 

data/lib/scbi_blast/batch_blast.rb

@@ -1,5 +1,5 @@
 # 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
@@ -7,10 +7,10 @@
 # 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.
@@ -19,6 +19,7 @@
 # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
+# TODO - Hacer algo cuando llegan secuencias vacias
 
 # class to execute Blast without temporary files (it uses pipes)
 class BatchBlast
@@ -60,9 +61,13 @@ class BatchBlast
     end
 
     cmd = get_blast_cmd(fmt)
-    
-    res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
-    
+
+    if !seqs.empty?
+      res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
+    else
+      res=''
+    end
+
     # check if all sequences where processed
     if parse_output
       if fmt == :table
@@ -88,27 +93,28 @@ class BatchBlast
       end
 
     end
-    
+
     return res
-    
+
   end
-  
+
   def self.do_blast_cmd(seq_fasta, cmd)
     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 solo los 20 primeros nt.
-    IO.popen(cmd,'w+') {|blast|
-      blast.sync = true
-      blast.write(seq_fasta)
-      blast.close_write
-      res = blast.readlines
-      blast.close_read
-    }
-
-    if !$?.exitstatus.nil? && $?.exitstatus>0
-      raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+    if !seq_fasta.empty?
+      # Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se  encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
+      IO.popen(cmd,'w+') {|blast|
+        blast.sync = true
+        blast.write(seq_fasta)
+        blast.close_write
+        res = blast.readlines
+        blast.close_read
+      }
+
+      if !$?.exitstatus.nil? && $?.exitstatus>0
+        raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
+      end
     end
-
+    
     return res
 
   end

data/lib/scbi_blast/blast_streamxml_result.rb

@@ -28,6 +28,7 @@ class BlastStreamxmlResult < BlastResult
     
     # @state = nil # (values :in_query,:in_hit)
     
+    return if input.empty?
     
     if input.is_a?(Array)
       lines=input.join("\n")

data/lib/scbi_blast/blast_table_result.rb

@@ -32,7 +32,8 @@ class BlastTableResult < BlastResult
 
     super(input)
 
-
+    return if input.empty?
+    
     if input.is_a?(Array)
       lines=input
 
@@ -47,6 +48,8 @@ class BlastTableResult < BlastResult
   end
   
   def parse(lines)
+    
+    
     query_name=''
 
     lines.each do |line|

metadata

@@ -2,7 +2,7 @@
 name: scbi_blast
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.34
+  version: 0.0.37
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-04-30 00:00:00 Z
+date: 2012-11-28 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: xml-simple
@@ -95,7 +95,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: scbi_blast
-rubygems_version: 1.7.2
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 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.