bio-gff3 0.8.2 → 0.8.3

data/VERSION

@@ -1 +1 @@
-0.8.2
+0.8.3

data/bin/gff3-fetch

@@ -16,9 +16,10 @@ USAGE = <<EOM
 
     --translate     : output as amino acid sequence 
     --validate      : validate GFF3 file by translating
+    --fix           : check 3-frame translation and fix, if possible 
+    --fix-wormbase  : fix 3-frame translation on ORFs named 'gene1'
     --no-assemble   : output each record as a sequence -- NYI
     --add-phase     : output records using phase (useful w. no-assemble CDS to AA) --NYI
-    --fix           : check 3-frame translation and fix, if possible -- NYI
   
   type is any valid type in the GFF3 definition. For example:
 
@@ -142,6 +143,14 @@ opts = OptionParser.new() { |opts|
     $stop_on_error = true  # replace global in near future
   end
 
+  opts.on("--fix", "Fix frame errors in the GFF3 definition") do |v|
+    options.fix = true
+  end
+
+  opts.on("--fix-wormbase", "Wormbase fix gene1 frame error") do |v|
+    options.fix_wormbase = true
+  end
+
   # opts.on("-q", "--quiet", "Run quietly") do |q|
   #   options.quiet = q
   # end
@@ -174,6 +183,8 @@ ARGV.each do | fn |
   opts[:cache_components] = options.cache
   opts[:cache_records]    = options.cache
   opts[:fasta_filename] = fastafn if fastafn
+  opts[:fix_wormbase] = options.fix_wormbase
+  opts[:fix] = options.fix
   gffdb = Bio::GFFbrowser::GFFdb.new(fn,opts)
   gff = gffdb.assembler
   writer = Bio::GFFbrowser::FastaWriter.new(options.translate, options.validate)

data/bio-gff3.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gff3}
-  s.version = "0.8.2"
+  s.version = "0.8.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]

data/lib/bio/db/gff/gffassemble.rb

@@ -206,16 +206,20 @@ module Bio
         #   :reverse      : do reverse if reverse is indicated (default true)
         #   :complement   : do complement if reverse is indicated (default true)
         #   :phase        : do set CDS phase (default false, normally ignore)
-        #   :trim         : make sure sequence is multiple of 3 nucleotide bps (default false)
+        #   :trim         : make sure sequence is multiple of 3 nucleotide bps (default true)
         #
-        # there are two special options:
+        # special options:
         #
         #   :raw          : raw sequence (all above false)
-        #   :codonize     : codon sequence (reverse, complement and trim are true)
+        #   :codonize     : codon sequence (reverse, complement, and trim are true)
+        #   :fix          : fix errors (default false)
         #
-        def assemble sequence, startpos, reclist, options = { :phase=>false, :reverse=>true, :trim=>false, :complement=>true, :debug=>false }
+        def assemble sequence, startpos, reclist, options = { :phase=>false, :reverse=>true, :trim=>true, :complement=>true, :fix=>false, :debug=>false }
+          # default to nil, if not passed in
           do_debug = options[:debug]
           do_phase = options[:phase]
+          do_fix        = options[:fix]
+          # default to true, if not passed in
           do_reverse = (options[:reverse] == false ? false : true)
           do_trim    = (options[:trim] == false ? false : true)
           do_complement = (options[:complement] == false ? false : true)
@@ -274,18 +278,50 @@ module Bio
             ntseq = Bio::Sequence::NA.new(seq)
             seq = ntseq.forward_complement.upcase
           end
+          # This is the place to fix sequences (e.g. the Wormbase bug)
+          if do_fix or @options[:fix] or @options[:fix_wormbase]
+            if @options[:fix_wormbase] and rec0.id.index('gene1')==0
+              # Wormbase gene1 only, so ignore rest
+            else
+              test_frame = 0
+              ntseq = Bio::Sequence::NA.new(seq)
+              aaseq = ntseq.translate
+              if aaseq.count('*') > 1
+                test_frame = 1
+                seq = seq[1..-1] 
+                ntseq = Bio::Sequence::NA.new(seq)
+                aaseq = ntseq.translate
+                if aaseq.count('*') > 1
+                  test_frame = 2
+                  seq = seq[1..-1]
+                  ntseq = Bio::Sequence::NA.new(seq)
+                  aaseq = ntseq.translate
+                  raise 'Validation problem '+rec0.id if aaseq.count('*') > 1
+                end
+              end
+              if test_frame > 0
+                warn rec0.id,"Frame adjusted to #{test_frame} (fix)"
+              end
+            end
+          end
           if do_trim
             reduce = seq.size % 3
             seq = seq[0..(seq.size-1-reduce)] if reduce != 0
           end
+          if @options[:validate]
+            ntseq = Bio::Sequence::NA.new(seq)
+            aaseq = ntseq.translate
+            raise 'Validate translation problem '+rec0.id+"\n"+seq if aaseq.count('*') > 1
+          end
+
           retval = seq
           retval
         end
 
         # Patch a sequence together from a Sequence string and an array
         # of records and translate in the correct direction and frame. The options 
-        # are the same as for +assemble+.
-        def assembleAA sequence, startpos, reclist, options = { :phase=>false, :reverse=>true, :trim=>false, :complement=>true }
+        # are the same as for +assemble+, except :trim defaults to true.
+        def assembleAA sequence, startpos, reclist, options = { :phase=>false, :reverse=>true, :trim=>true, :complement=>true }
           seq = assemble(sequence, startpos, reclist, options)
           ntseq = Bio::Sequence::NA.new(seq)
           ntseq.translate

data/lib/bio/output/gfffastawriter.rb

@@ -10,11 +10,11 @@ module Bio
 
       def put id, seq
         puts '>'+id
-        put_seq seq
+        put_seq id, seq
       end
       private
 
-      def put_seq seq
+      def put_seq id, seq
         if @do_translate or @do_validate
           ntseq = Bio::Sequence::NA.new(seq)
           aaseq = ntseq.translate

data/spec/gff3_assemble3_spec.rb

@@ -30,7 +30,6 @@ describe GFFdb, "Assemble CDS (extra checks)" do
     name = "cds:MhA1_Contig1040.frz3.gene"
     recs = @cdslist[name]
     component = @componentlist[name]
-    p recs
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
     ntseq.should == "TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAA"
     ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
@@ -56,6 +55,26 @@ describe GFFdb, "Assemble CDS (extra checks)" do
     aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
     aaseq.should == "KINKKINDNSFNIQSDSNENLFNDGINSEQNEDNIATKKGNKKFGKNQKEGNKELDIQSEGFDNNEIPSKESKKQISNFGDNESEYEKEEDNRKKKGKKGMIEKYELGRNKGRDKNERNKASERFDEQNQDRNNQRDSFDSGNNDKSQRGLDSGTLDGTNNLKRSNDDQLPEFLKTASLSERQKFLQLEAENDRSKSSIRRDKQNWADQQGQRISDLYKQFQQSLQQKEKQFKSERQRNVQIKLSRNAQNVDKRIQDLLNNPDIAERALILQIEQILGGTDDSIRQELQRQISVIGPLDGNIPPNLT*"
   end
+  it "should fix Wormbase error MhA1_Contig3426.frz3.gene1" do
+    @contigsequence = @gff.sequencelist["MhA1_Contig3426"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+    name = "cds:MhA1_Contig3426.frz3.gene1"
+    recs = @cdslist[name]
+    component = @componentlist[name]
+    # :raw should not fix
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
+    ntseq.should == "GCATCCAACAACAACAATTAGAAGTCTTTCCCAGCTCCTCCTCTGCCCCTCAGCAACAACAATACCCAGCGCAGCAGCTTCAATTAGTTACTCCTTTTATTGCATGCATAGCAGATGAATTGAGGGAGTTGATAGATGAAATGCGTATGTTTTAG"
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true,:fix=>true)
+    ntseq.should == "ATCCAACAACAACAATTAGAAGTCTTTCCCAGCTCCTCCTCTGCCCCTCAGCAACAACAATACCCAGCGCAGCAGCTTCAATTAGTTACTCCTTTTATTGCATGCATAGCAGATGAATTGAGGGAGTTGATAGATGAAATGCGTATGTTTTAG"
+    ntseq.size.should == 153
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs,:fix=>true)
+    aaseq.should == "IQQQQLEVFPSSSSAPQQQQYPAQQLQLVTPFIACIADELRELIDEMRMF*"
+  end
 end
 
 

data/spec/gff3_assemble_spec.rb

@@ -77,7 +77,7 @@ describe GFFdb, "Assemble CDS" do
     component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
     cds0 = recs[0]
     cds0.seqname.should == 'MhA1_Contig1133'
-    seq = @gff.assemble(@contigsequence,component.start,[cds0])
+    seq = @gff.assemble(@contigsequence,component.start,[cds0],:trim=>false)
     seq.size.should == 143
     seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAG"
     aaseq = @gff.assembleAA(@contigsequence,component.start,[cds0])
@@ -88,7 +88,7 @@ describe GFFdb, "Assemble CDS" do
     recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
     component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
     cds1 = recs[1]
-    seq = @gff.assemble(@contigsequence,component.start,[cds1])
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:trim=>false)
     seq.size.should == 244
     seq.should == "TGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
     seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase => true)

data/test/data/gff/test-cds.gff3

@@ -9,6 +9,8 @@ ene29.1;Parent=transcript:MhA1_Contig1040.frz3.gene29
 MhA1_Contig1040	WormBase	CDS	1	180	.	-	2	ID=cds:MhA1_Contig1040.frz3.gene
 29;Parent=transcript:MhA1_Contig1040.frz3.gene29
 
+
+
 ##gff-version 3 ##sequence-regio
 # Gene gene:MhA1_Contig2992.frz3.gene1
 MhA1_Contig2992	WormBase	gene	577	2176	.	-	.	ID=gene:MhA1_Contig2992.frz3.gene1;Name=MhA1_Contig2992.frz3.gene1;Note=PREDICTED protein_coding;public_name=MhA1_Contig2992.frz3.gene1
@@ -50,6 +52,13 @@ MhA1_Contig2992	RepeatMask	repeat_region	2957	3019	28	+	.	ID=RepeatMask.324638
 MhA1_Contig2992	Dust	repeat_region	2959	3019	.	-	.	ID=Dust.42112
 MhA1_Contig2992	RepeatMask	repeat_region	3194	3237	23	+	.	ID=RepeatMask.324639
 MhA1_Contig2992	Dust	repeat_region	3222	3277	.	-	.	ID=Dust.42114
+##gff-version 3
+##sequence-region MhA1_Contig3426 1 2029
+# Gene gene:MhA1_Contig3426.frz3.gene1
+MhA1_Contig3426	WormBase	gene	192	346	.	+	.	ID=gene:MhA1_Contig3426.frz3.gene1;Name=MhA1_Contig3426.frz3.gene1;Note=PREDICTED protein_coding;public_name=MhA1_Contig3426.frz3.gene1
+MhA1_Contig3426	WormBase	mRNA	192	346	.	+	.	ID=transcript:MhA1_Contig3426.frz3.gene1;Parent=gene:MhA1_Contig3426.frz3.gene1;Name=MhA1_Contig3426.frz3.gene1;public_name=MhA1_Contig3426.frz3.gene1
+MhA1_Contig3426	WormBase	exon	192	346	.	+	.	ID=exon:MhA1_Contig3426.frz3.gene1.1;Parent=transcript:MhA1_Contig3426.frz3.gene1
+MhA1_Contig3426	WormBase	CDS	192	346	.	+	0	ID=cds:MhA1_Contig3426.frz3.gene1;Parent=transcript:MhA1_Contig3426.frz3.gene1
 ##FASTA
 >MhA1_Contig2992
 TTTTGGTGACCAAAGTTCCTATTGGTGACCAAAATTCCAGTGCCCAATATTCCGTTTTTTGACTTGGTGACCAAAATTCC
@@ -96,3 +105,9 @@ TATTTTTTGTTAAATAAAAGGTTTAAATTAATTATTTGTGCTTTTTCGAATTTTTCATTTAAATCCTTTATTTTTTTGAA
 ATTATCATAAAGCTCTAATGATGCTTTTTGAATTTTTGAGACATTTTCAATATCAAAATTTGGTCCGGAAAATTTATTTA
 >MhA1_Contig1040
 TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAAAC
+>MhA1_Contig3426
+TTAATAAATTTAATTCATTAAAATTTTAAAAAGAAAGGGACATTCGAGGGGAAATGAGAGAGAACGAGAGAAAATGGACG
+GGAAATTAAATTAAAAAATAAAAAATTAATTTTTATTTTTTTTTATTTAATTTAAAATTAATTTTCTACATTTATTAAAT
+CTTAAATTATTAATTTTAAATTAATTTAAAG GCATCCAACAACAACAATTAGAAGTCTTTCCCAGCTCCTCCTCTGCCCC
+TCAGCAACAACAATACCCAGCGCAGCAGCTTCAATTAGTTACTCCTTTTATTGCATGCATAGCAGATGAATTGAGGGAGT
+TGATAGATGAAATGCGTATGTTTTAG AATATTTTTTAAAAAAAAATTAAAAAAAATTTTTTTTTGCCAAACAGGCTCTCG

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 8
-  - 2
-  version: 0.8.2
+  - 3
+  version: 0.8.3
 platform: ruby
 authors: 
 - Pjotr Prins
@@ -180,7 +180,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -876270257
+      hash: -450771567
       segments: 
       - 0
       version: "0"