bio-synreport 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bio-synreport.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-synreport}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]

data/lib/bio/utils/bio-synreport.rb

@@ -5,7 +5,6 @@ require 'bio'
 module Bio
   class Util
     
-<<<<<<< HEAD
     class MrnaModel < Bio::GFF::GFF3::Record
       attr_accessor :seq, :cds
       def initialize(gff_line)
@@ -78,69 +77,15 @@ module Bio
             return {#:id => self.gffid, 
                     :chr => self.seqname, 
                     :strand => self.strand, 
-=======
-    class MrnaModel
-      attr_accessor :seqname, :gff_id, :strand, :cds, :sequences
-  
-      def initialize(chr, id, strand, cds_arr, seq_arr)
-        @seqname, @gff_id, @strand, @cds, @sequences = chr, id, strand, cds_arr, seq_arr
-      end
-  
-      def includes?(seq, point)
-        @cds.each {|start, stop| return true if @seqname == seq and point.to_i >= start and point.to_i <= stop}
-        false
-      end
-  
-      def seq
-        @sequences.join
-      end
-  
-      def substitution_info(chr,point,alt)
-        cds_start = @cds.first.first
-        running_total = 0
-        @cds.each do |start,stop|
-          if point.to_i >= start and point.to_i <= stop
-            offset = case @strand
-            when "+"
-              #offset = 
-              (point.to_i - start) + running_total
-            when "-"
-              (stop - point.to_i) + running_total 
-            end  #offset = how far into cds SNP is
-            codon_number = offset / 3
-            position_in_codon = offset % 3
-            #pp [offset, codon_number, position_in_codon] 
-            codon_array = []; Bio::Sequence::NA.new(self.seq).window_search(3,3) {|b| codon_array << b}
-            codon = codon_array[codon_number]
-            nt = codon[position_in_codon]
-            new_codon = codon.dup
-            new_codon[position_in_codon] = alt.downcase
-            #pp [codon, position_in_codon, nt, new_codon]
-            a = Bio::Sequence::NA.new(codon).translate.codes.first
-            b =  Bio::Sequence::NA.new(new_codon).translate.codes.first
-            sub_type = a == b ? "SYN" : "NON_SYN"
-            return {:id => @gff_id, 
-                    :chr => @seqname, 
-                    :strand => @strand, 
->>>>>>> 188a1a611ad6334046551c7bba186dc1c7ae85af
                     :position => point,
                     :original_codon => codon, 
                     :original_residue => a || 'stop', 
                     :mutant_codon => new_codon, 
                     :mutant_residue =>b || 'stop', 
-<<<<<<< HEAD
                     :position_in_codon => position + 1, 
                     :substitution_type => sub_type
                     }
-=======
-                    :position_in_codon => position_in_codon + 1, 
-                    :substitution_type => sub_type
-                    }
-          end
-          running_total += (stop - start)
-          running_total += 1 if @strand == '-' #how far we are into the cds
-        end
->>>>>>> 188a1a611ad6334046551c7bba186dc1c7ae85af
+
       end
       
     end#class end
@@ -150,7 +95,6 @@ module Bio
       #attr_accessor :cdshash, :cds_list, :mRNAhash, :seqhash
       
       def initialize(opts)
-<<<<<<< HEAD
         cdses = []
         mrna_list = []
         seqs = Hash.new
@@ -190,68 +134,10 @@ module Bio
         
         def is_in_cds?(chr,point)
           self.mutation_info(chr,point,"a") ? true : false
-=======
-        @gene_array = []
-        @cdshash = Hash.new {|h,k| h[k] = Hash.new {|a,b| a[b] = [] } }
-        @mRNAhash = Hash.new {|h,k| h[k] = Hash.new {|a,b| a[b] = [] } }
-        File.open(opts[:gff], "r").each do |gffline|
-          record=Bio::GFF::GFF3::Record.new(gffline)
-          if(record.feature_type == 'gene')
-              @gene_array << [record.seqname, record.id]
-          elsif(record.feature_type == 'CDS' or record.feature_type == 'mRNA')
-            parents = record.get_attributes('Parent')
-            parents.each do |parent|  
-              if record.feature_type == 'CDS'
-                @cdshash[record.seqname][parent] << record
-              else
-                @mRNAhash[record.seqname][parent] << record
-              end
-            end
-          end
-        end
-        $stderr.puts "Loaded GFF..." if opts[:verbose]
-        @seqhash = {}
-        Bio::FastaFormat.open(opts[:fasta]).each { |seq| @seqhash[seq.entry_id] = seq.to_seq }
-        $stderr.puts "Loaded Seq..." if opts[:verbose]
-        
-        @models = Hash.new {|h,k| h[k] =  []  }
-        $stderr.puts "Building models..." if opts[:verbose] 
-        @gene_array.each do |gene|
-
-          mRNAs=@mRNAhash[gene.first][gene.last]
-          mRNAs.each do |mRNA|
-            next if @seqhash[gene.first].nil?
-            cdsa = []
-            seqs = []
-            cdsary=@cdshash[gene.first][mRNA.id]
-            cdsary.each {|c| cdsa << [c.start, c.end]} 
-            cdsa.sort!
-            cdsa.reverse! if mRNA.strand == '-'
-            
-            cdsa.each do |cds|
-
-              #cdsa << [cds.start, cds.end]
-              if mRNA.strand == '+'
-                seqs << Bio::Sequence::NA.new(@seqhash[mRNA.seqname].splicing("#{cds.first}..#{cds.last}") )
-              elsif mRNA.strand == "-"
-                seqs << Bio::Sequence::NA.new(@seqhash[mRNA.seqname].splicing("#{cds.first}..#{cds.last}") ).complement
-              end
-            end
-            @models[mRNA.seqname] << Bio::Util::MrnaModel.new(mRNA.seqname, mRNA.id, mRNA.strand, cdsa, seqs )
-            #pp @models[mRNA.seqname][-1].cds if mRNA.id == 'AT2G17530.1' or mRNA.id == 'AT2G17550.1'
-          end
-        end
-        $stderr.puts "Models built..." if opts[:verbose]
-      end#init end
-        
-        def is_in_cds?(chr,point)
-          @self.mutation_info(chr,point) ? true : false
->>>>>>> 188a1a611ad6334046551c7bba186dc1c7ae85af
         end
         
         #returns mutation info if point in CDS, if not in CDS returns false
         def mutation_info(chr,pos,alt)
-<<<<<<< HEAD
           pos = pos.to_i
           #cant do indels ...
           return nil if alt.length > 1
@@ -266,15 +152,6 @@ module Bio
             #somthing unpredicatable went wrong and we couldnt do the conversion ...
             return nil
           end
-=======
-
-          @models[chr].each do |m|
-             if m.includes?(chr,pos)
-               return m.substitution_info(chr,pos,alt)   
-             end
-          end
-          false
->>>>>>> 188a1a611ad6334046551c7bba186dc1c7ae85af
         end
         
         

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 1
-  version: 0.1.1
+  - 2
+  version: 0.1.2
 platform: ruby
 authors: 
 - Dan MacLean