scbi_fasta 0.1.8 → 0.1.9

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.1.9 2011-10-28
+
+Also parses and returns comment lines in each and nextseq
+
 === 0.1.8 2011-06-13
 
 first rubygems published

data/lib/scbi_fasta.rb

@@ -8,5 +8,5 @@ require 'fasta_file'
 
 
 module ScbiFasta
-   VERSION = '0.1.8'
+   VERSION = '0.1.9'
 end

data/lib/scbi_fasta/fasta_qual_file.rb

@@ -34,11 +34,12 @@ attr_accessor :num_seqs, :end_fasta
   		@with_qual = false
       #raise "File #{qual_file_name} doesn't exists" 
   	end
-  
+  # puts "With_qual #{fasta_file_name}?: #{@with_qual}"
   		
       @num_seqs = 0 ;      
       
       @seq_name = '';      
+      @seq_comment='';
       @file_fasta = File.open(fasta_file_name) ;
       @end_fasta=false;
       
@@ -67,16 +68,17 @@ attr_accessor :num_seqs, :end_fasta
         
     rewind
 
-	  n,f,q=next_seq
+	  n,f,q,c = next_seq
     while (!n.nil?)
 	  
 					if @with_qual
-						yield(n,f,q)
+
+						yield(n,f,q,c)
 					else
-					  yield(n,f)
+					  yield(n,f,q)
 					end
 					
-  				n,f,q=next_seq
+  				n,f,q,c=next_seq
     end
 
   	rewind
@@ -89,6 +91,7 @@ attr_accessor :num_seqs, :end_fasta
      @num_seqs = 0 ;      
      
      @seq_name = '';      
+     @seq_comment= '';
      @file_fasta.pos=0
      @end_fasta=false;
 
@@ -111,7 +114,7 @@ attr_accessor :num_seqs, :end_fasta
 	  # envia on_process_sequence
     if ((!@end_fasta) && (!@with_qual or !@end_qual))
 
-	      name_f,fasta=read_fasta 
+	      name_f,fasta,comment=read_fasta 
   	    
         if @with_qual
 					  
@@ -129,9 +132,9 @@ attr_accessor :num_seqs, :end_fasta
 							if fasta.length == qual.count(' ') + 1
 								if @qual_to_array
 									a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
-									res =[name_f,fasta,a_qual]
+									res =[name_f,fasta,a_qual,comment]
 								else
-									res =[name_f,fasta,qual]
+									res =[name_f,fasta,qual,comment]
 								end
 						
 							else #if (!a_qual.empty?)
@@ -141,7 +144,7 @@ attr_accessor :num_seqs, :end_fasta
             end
 				 
         else # without qual				 
-				 		res =[name_f,fasta]
+				 		res =[name_f,fasta,comment]
         end
     end
   	
@@ -179,17 +182,19 @@ attr_accessor :num_seqs, :end_fasta
         if !@seq_name.empty?
           # ya había leido una
           #puts "leida #{@seq_name} + #{@seq_fasta}"
-          res = [@seq_name,seq_fasta]
+          res = [@seq_name,seq_fasta, @seq_comment]
         end
 
 
         #get only name
         line_fasta.gsub!(/^>\s*/,'');
         
-        line_fasta =~ /(^[^\s]+)/
+        # line_fasta =~ /(^[^\s]+)/
+        line_fasta =~ /(^[^\s]+)\s*(.*)$/
         # remove comments
         
         @seq_name = $1
+        @seq_comment = $2
         
         seq_fasta='';
         
@@ -211,7 +216,7 @@ attr_accessor :num_seqs, :end_fasta
     
     #si no hay más secuencias hay que devolver la última, CASO EOF
     if res.nil? and !@seq_name.empty?
-      res= [@seq_name,seq_fasta]
+      res= [@seq_name,seq_fasta, @seq_comment]
     end
     
     return res

data/test/test_fasta_qual_file.rb

@@ -4,7 +4,7 @@ class TestFastaQualFile < Test::Unit::TestCase
 
 
   def setup
-    @test_file='/tmp/fbinfile';
+    @test_file='/tmp/scbi_fasta';
 
     @seq_fasta='ACTG'
     @seq_qual=[25]
@@ -19,7 +19,7 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     n.times do |c|
       i = c+1
-      name = ">#{@seq_name+i.to_s} comments"
+      name = ">#{@seq_name+i.to_s} comments#{i}"
 
       f.puts(name)
       f.puts(@seq_fasta*i)
@@ -46,13 +46,13 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     100.times do |c|
       i = c+1
-      n,s,q = fqr.next_seq
+      n,s,q,c = fqr.next_seq
 
       #puts n,s.length,q.split(' ').length
-      assert(@seq_name+i.to_s==n)
-      assert(@seq_fasta*i==s)
-      assert((@seq_qual*i*@seq_fasta.length).join(' ')==q)
-
+      assert_equal(@seq_name+i.to_s,n)
+      assert_equal(@seq_fasta*i,s)
+      assert_equal((@seq_qual*i*@seq_fasta.length).join(' '),q)
+      assert_equal('comments'+i.to_s,c)
     end
 
     fqr.close
@@ -74,13 +74,13 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     i=1
 
-    fqr.each do |n,s,q|
+    fqr.each do |n,s,q,c|
 
       #puts n,s.length,q.split(' ').length
-      assert(@seq_name+i.to_s==n)
-      assert(@seq_fasta*i==s)
-      assert((@seq_qual*i*@seq_fasta.length).join(' ')==q)
-
+      assert_equal(@seq_name+i.to_s,n)
+      assert_equal(@seq_fasta*i,s)
+      assert_equal((@seq_qual*i*@seq_fasta.length).join(' '),q)
+      assert_equal('comments'+i.to_s,c)
       i+=1
     end
 
@@ -105,11 +105,12 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     100.times do |c|
       i = c+1
-      n,s,q = fqr.next_seq
+      n,s,c,q = fqr.next_seq
 
-      #puts n,s.length,q.split(' ').length
-      assert(@seq_name+i.to_s==n)
-      assert(@seq_fasta*i==s)
+      # puts n,s.length,q.split(' ').length
+      assert_equal(@seq_name+i.to_s,n)
+      assert_equal(@seq_fasta*i,s)
+      assert_equal('comments'+i.to_s,c)
       assert(q.nil?)
 
     end
@@ -135,12 +136,12 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     i=1
 
-    fqr.each do |n,s,q|
-
+    fqr.each do |n,s,c,q|
+       # puts n,s,q
       #puts n,s.length,q.split(' ').length
-      assert(@seq_name+i.to_s==n)
-      assert(@seq_fasta*i==s)
-
+      assert_equal(@seq_name+i.to_s,n)
+      assert_equal(@seq_fasta*i,s)
+      assert_equal('comments'+i.to_s,c)
       assert(q.nil?)
 
       i+=1
@@ -150,10 +151,10 @@ class TestFastaQualFile < Test::Unit::TestCase
 
     fqr.close
 
-  rescue Exception => e
-    puts "failed in #{n} , #{s}"
-    puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
-    puts e.message, e.backtrace
+  # rescue Exception => e
+  #   puts "failed in #{n} , #{s}"
+  #   puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
+  #   puts e.message, e.backtrace
 
   end
 

metadata

@@ -2,7 +2,7 @@
 name: scbi_fasta
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.1.8
+  version: 0.1.9
 platform: ruby
 authors: 
 - Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-13 00:00:00 Z
+date: 2011-10-28 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: hoe