scbi_blast 0.0.42 → 0.0.43

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.43 2014-01-24
+
+Fix last comment checkout
+
 === 0.0.42 2013-09-19
 
 Using PTY to avoid blocking of popen in newer systems

data/lib/scbi_blast.rb

@@ -48,7 +48,7 @@ require 'blast_hit'
 require 'blast_table_result'
 
 module ScbiBlast
-   VERSION = '0.0.42'
+   VERSION = '0.0.43'
 end
 
 

data/lib/scbi_blast/batch_blast.rb

@@ -83,9 +83,12 @@ class BatchBlast
       res=''
     end
 
+
+
     # check if all sequences where processed
     if parse_output
       if fmt == :table
+
         res = BlastTableResult.new(res)
       elsif fmt == :xml
         res = BlastStreamxmlResult.new(res)
@@ -104,7 +107,7 @@ class BatchBlast
           end
         end
 
-        raise "These sequences #{seq_fasta.count('>')},#{res.querys.count} where not processed by #{cmd}:\n #{not_processed} \n Full_data:\n seqs=#{seqs};\n"
+        raise "If using table format, please, use format 7. These queries where empty or not processed: #{seq_fasta.count('>')},#{res.querys.count}  by CMD: #{cmd}:\n #{not_processed} \n Full_data:\n seqs=#{seqs};\n"
       end
 
     end

data/lib/scbi_blast/blast_table_result.rb

@@ -49,8 +49,13 @@ class BlastTableResult < BlastResult
   
   def parse(lines)
     
-    if !(lines.last =~ /# BLAST processed (\d+) queries/)
-      raise "Blast didn't processed your queries"
+    with_comments=false
+
+    if lines.first.index('#')==0 
+        with_comments=true
+        if !(lines.last =~ /# BLAST processed (\d+) queries/)
+            raise "Blast didn't processed your queries"
+        end
     end
     
     query_name=''
@@ -112,6 +117,12 @@ class BlastTableResult < BlastResult
         # else the hit will be added to the last query
 
         qseqid,sacc,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,score,qframe,sframe,qseq,sseq,qlen,slen,stitle = params
+        
+        # if format6 
+        #if !with_comments and query_name!=qseqid
+        #    @querys.push BlastQuery.new(query_name)
+        #    query_name=qseqid
+        #end
 
         # creates the hit
         hit = BlastHit.new(qstart,qend,sstart,send)

data/test/test_scbi_blast.rb

@@ -119,6 +119,14 @@ class TestScbiBlast < Test::Unit::TestCase
       assert_equal(999,res.querys.count)
       
   	
+  end
+
+  def test_good_table_sin_c
+      res = BlastTableResult.new(File.join(File.dirname(__FILE__),'table_sin_c.txt'))
+      # the rest of querys up to 999 are empty
+      assert_equal(391,res.querys.count)
+      
+    
   end
 
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: scbi_blast
 version: !ruby/object:Gem::Version
-  version: 0.0.42
+  version: 0.0.43
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-24 00:00:00.000000000 Z
+date: 2014-01-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: xml-simple
@@ -66,7 +66,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.6'
+        version: '3.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -74,7 +74,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.6'
+        version: '3.7'
 description: ! "scbi_blast is a ruby gem to handle blast+ executions using pipes when
   possible to read data without the need of temporary files, \nit has been developed
   at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero."
@@ -113,7 +113,8 @@ files:
 - lib/scbi_blast/dust_masker.rb
 - .gemtest
 homepage: http://www.scbi.uma.es/downloads
-licenses: []
+licenses:
+- MIT
 post_install_message: 
 rdoc_options:
 - --main
@@ -134,12 +135,12 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: scbi_blast
-rubygems_version: 1.8.24
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: scbi_blast is a ruby gem to handle blast+ executions using pipes when possible
   to read data 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
+- test/test_helper.rb