scbi_cominer 0.0.3 → 0.0.4

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.4 2012-09-25
+
+Added offsets
+
 === 0.0.3 2012-09-25
 
 upcase in freqtable

data/lib/scbi_cominer/classes/frequency_table.rb

@@ -97,20 +97,27 @@ class FrequencyTable
   end
 
   def add_read(read)
-    add_fasta(read.name, read.fasta)
+    add_fasta(read.name, read.fasta, read.start_in_consensus, read.align_clip_start, read.align_clip_end)
   end
 
-  def add_sequence(seq)
+  def add_sequence(seq, offset)
     add_fasta(seq.seq_name,seq.seq_fasta)
   end
 
-  def add_fasta(name,fasta)
+  def add_fasta(name,fasta, in_consensus_offset, align_clip_start, align_clip_end)
 
     @sequences.push({:name=>name,:fasta=>fasta})
     index = @sequences.length
-
-    i = 0
-    fasta.upcase.each_char do |c|
+    
+    fasta_u=fasta.upcase
+    
+    i = (align_clip_start.to_i+in_consensus_offset.to_i)-1
+    
+    # seq_i=in_seq_offset.to_i
+    
+    # while !(c=fasta_u[seq_i]).nil?
+    # puts ("_"*i+fasta[align_clip_start.to_i-1..align_clip_end.to_i-1])[0..80]+'...'
+    fasta[align_clip_start.to_i-1..align_clip_end.to_i-1].upcase.each_char do |c|
 
       #get current freq
       freq = @frequency_table[c]
@@ -221,6 +228,8 @@ class FrequencyTable
 
   def inspect
 
+    # return  @frequency_table.to_json
+    
     res = ''
 
     @frequency_table.each do |c,v|

data/lib/scbi_cominer/cominer.rb

@@ -12,12 +12,14 @@ class Cominer
     @freq_table = FrequencyTable.new
   
   	contig.reads.each do |name,read|
-      # puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end}"
+      # puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end} #{read.start_in_consensus}"
+      # puts read.fasta[read.align_clip_start.to_i..read.align_clip_end.to_i]
       # puts read.fasta
   		@freq_table.add_read(read)
   	end
   	
-    # puts freq_table.inspect
+    puts freq_table.inspect
+    exit
   	
   	ef = EntropyFunction.new(@freq_table)
    

data/lib/scbi_cominer.rb

@@ -8,5 +8,5 @@ $: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FIL
 require 'cominer.rb'
 
 module ScbiCominer
-   VERSION = '0.0.3'
+   VERSION = '0.0.4'
 end

data/test/test_scbi_cominer.rb

@@ -23,10 +23,11 @@ class TestScbiCominer < Test::Unit::TestCase
       cominer_stats=Cominer.new(contig)
       
       
+      
       # get all reads with orientation and align clips
       contig.reads.each do |name,read|
-    	  puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end}"
-    	  puts read.fasta
+    	  puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end} #{read.start_in_consensus}"
+    	  puts read.fasta[read.align_clip_start.to_i..read.align_clip_end.to_i]
     	end
 
       # get position_table

metadata

@@ -2,7 +2,7 @@
 name: scbi_cominer
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors: 
 - Dario Guerrero