bio-gff3 0.6.0 → 0.8.0

data/Gemfile

@@ -11,4 +11,5 @@ group :development do
   gem "jeweler", "~> 1.5.2"
   gem "rcov", ">= 0"
   gem "bio", ">= 1.4.1"
+	gem "rspec"
 end

data/Gemfile.lock

@@ -2,6 +2,7 @@ GEM
   remote: http://rubygems.org/
   specs:
     bio (1.4.1)
+    diff-lcs (1.1.2)
     git (1.2.5)
     jeweler (1.5.2)
       bundler (~> 1.0.0)
@@ -9,6 +10,14 @@ GEM
       rake
     rake (0.8.7)
     rcov (0.9.9)
+    rspec (2.3.0)
+      rspec-core (~> 2.3.0)
+      rspec-expectations (~> 2.3.0)
+      rspec-mocks (~> 2.3.0)
+    rspec-core (2.3.1)
+    rspec-expectations (2.3.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.3.0)
     shoulda (2.11.3)
 
 PLATFORMS
@@ -19,4 +28,5 @@ DEPENDENCIES
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
   rcov
+  rspec
   shoulda

data/README.rdoc

@@ -1,19 +1,69 @@
 = bio-gff3
 
-Description goes here.
-
-== Contributing to bio-gff3
- 
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+GFF3 plugin for BioRuby, aimed at parsing big data
+
+Features:
+
+# Take GFF (genome browser) information and digest mRNA and CDS sequences
+# Options for low memory use and caching of records
+# Support for external FASTA files
+
+You can use this plugin in two ways. First as a standalone program, next as a
+plugin library to BioRuby.
+
+For example, fetch mRNA and CDS information from GFF3 files and output to FASTA:
+
+  ./bin/gff3-fetch mrna test/data/gff/test.gff3
+  ./bin/gff3-fetch cds test/data/gff/test.gff3
+
+Or clone this repository and add the 'lib' dir to the Ruby search path and 
+
+  require 'bio/db/gff/gffdb'
+
+You can also run RSpec with something like
+
+  rspec -I ../bioruby/lib/ spec/*.rb 
+
+This implementation depends on BioRuby's basic GFF3 parser, with the possible
+advantage that the plugin is faster and does not consume all memory. The Gff3
+specs are based on the output of the Wormbase genome browser.
+
+For a write-up see http://thebird.nl/bioruby/BioRuby_GFF3.html 
+
+-------------------------------------------------------------------------------
+
+
+  Fetch and assemble mRNAs, or CDS and print in FASTA format. 
+
+    gff3-fetch [--no-cache] mRNA|CDS [filename.fa] filename.gff
+
+  Where:
+
+    --no-cache      : do not load everything in memory (slower)
+    mRNA            : assemble mRNA
+    CDS             : assemble CDS 
+
+  Multiple GFF3 files can be used. For external FASTA files, always the last
+  one before the GFF file is used.
+
+  Examples:
+
+    Find mRNA and CDS information from test.gff3 (which includes sequence information)
+
+      gff3-fetch mRNA test/data/gff/test.gff3
+      gff3-fetch CDS test/data/gff/test.gff3
+
+    Find CDS from external FASTA file
+
+      gff3-fetch CDS test/data/gff/MhA1_Contig1133.fa test/data/gff/MhA1_Contig1133.gff3
+
+    Find mRNA from external FASTA file, without loading everything in RAM
+
+      gff3-fetch --no-cache mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+
+  If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
 
 == Copyright
 
-Copyright (c) 2010 Pjotr Prins. See LICENSE.txt for
-further details.
+Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl> 
 

data/VERSION

@@ -1 +1 @@
-0.6.0
+0.8.0

data/bin/gff3-fetch

@@ -4,7 +4,7 @@
 # Copyright:: August 2010
 # License:: Ruby License
 #
-# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+# Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>
 
 
 USAGE = <<EOM
@@ -14,7 +14,7 @@ USAGE = <<EOM
 
   Where:
 
-    --no-cache      : do not load everything in memory 
+    --no-cache      : do not load everything in memory (slower)
     mRNA            : assemble mRNA
     CDS             : assemble CDS 
 
@@ -25,19 +25,22 @@ USAGE = <<EOM
 
     Find mRNA and CDS information from test.gff3 (which includes sequence information)
 
-      ./bin/gff3-fetch mRNA test/data/gff/test.gff3
-      ./bin/gff3-fetch CDS test/data/gff/test.gff3
+      gff3-fetch mRNA test/data/gff/test.gff3
+      gff3-fetch CDS test/data/gff/test.gff3
 
-    Find CDS from exteranl FASTA file
+    Find CDS from external FASTA file
 
-      ./bin/gff3-fetch cds test/data/gff/MhA1_Contig1133.fa test/data/gff/MhA1_Contig1133.gff3
+      gff3-fetch CDS test/data/gff/MhA1_Contig1133.fa test/data/gff/MhA1_Contig1133.gff3
 
     Find mRNA from external FASTA file, without loading everything in RAM
 
-      ./bin/gff3-fetch --no-cache mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+      gff3-fetch --no-cache mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
 
   If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
 
+== Copyright
+
+Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl> 
 
 EOM
 
@@ -45,9 +48,9 @@ rootpath = File.dirname(File.dirname(__FILE__))
 $: << rootpath+'/lib'
 $: << rootpath+'/../bioruby/lib'
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
-$stderr.print "BioRuby GFF3 Plugin Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
+$stderr.print "BioRuby GFF3 Plugin Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
 
 if ARGV.size == 0
   print USAGE

data/bio-gff3.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gff3}
-  s.version = "0.6.0"
+  s.version = "0.8.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = %q{2010-12-29}
+  s.date = %q{2010-12-31}
   s.default_executable = %q{gff3-fetch}
   s.description = %q{GFF3 (genome browser) information and digest mRNA and CDS sequences.
 Options for low memory use and caching of records.
@@ -19,14 +19,12 @@ Support for external FASTA files.
   s.executables = ["gff3-fetch"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
-    "README",
     "README.rdoc"
   ]
   s.files = [
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
-    "README",
     "README.rdoc",
     "Rakefile",
     "VERSION",
@@ -83,12 +81,14 @@ Support for external FASTA files.
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<rspec>, [">= 0"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
@@ -96,6 +96,7 @@ Support for external FASTA files.
     s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<rspec>, [">= 0"])
   end
 end
 

data/lib/bio-gff3.rb

@@ -0,0 +1 @@
+require 'bio/db/gff/gffdb'

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

@@ -198,77 +198,76 @@ module Bio
         # to the landmark given in column 1 - in this case the sequence as it
         # is passed in. The following options are available:
         #
-        #   :phase        : set phase (default true)
-        #   :reverse      : do reverse if reverse is indicated (true)
-        #   :complement   : do complement if reverse is indicated (true)
-        #   :trim         : make sure sequence is multiple of 3 nucleotide bps (false)
+        #   :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)
         #
         # there are two special options:
         #
         #   :raw          : raw sequence (all above false)
-        #   :codonize     : codon sequence (all above true)
+        #   :codonize     : codon sequence (reverse, complement and trim are true)
         #
-        def assemble sequence, startpos, reclist, options = { :phase=>true, :reverse=>true, :trim=>false, :complement=>false }
+        def assemble sequence, startpos, reclist, options = { :phase=>false, :reverse=>true, :trim=>false, :complement=>true, :debug=>false }
+          do_debug = options[:debug]
           do_phase = options[:phase]
-          do_reverse = options[:reverse]
-          do_trim = options[:trim]
-          do_complement = options[:complement]
+          do_reverse = (options[:reverse] == false ? false : true)
+          do_trim    = (options[:trim] == false ? false : true)
+          do_complement = (options[:complement] == false ? false : true)
           if options[:raw]
             do_phase = false
             do_reverse = false
             do_trim = false
             do_complement = false
           elsif options[:codonize]
-            do_phase = true
+            do_phase = false
             do_reverse = true
             do_trim = true
             do_complement = true
           end
-          retval = ""
           sectionlist = Sections::sort(reclist)
-          reverse = false
-          # we assume strand is always the same
           rec0 = sectionlist.first.rec
-          reverse = (rec0.strand == '-') if rec0.strand
-          if reverse
-            # fetch phase from the last feature when reversed
-            rec0 = sectionlist.last.rec
-          end
-          frame = 0
-          frame = rec0.frame if rec0.frame
-          sectionlist.each do | section |
-            if sequence.kind_of?(Bio::FastaFormat)
-              sequence = sequence.seq
-            end
-            rec = section.rec
-            seq = sequence[(rec.start-1)..(rec.end-1)]
-            retval += seq
+          # we assume ORF is always read in the same direction
+          orf_reverse = (rec0.strand == '-')
+          orf_frame = startpos - 1
+          orf_frameshift = orf_frame % 3
+          sectionlist = sectionlist.reverse if orf_reverse
+          if do_debug
+            p "------------------"
+            p options 
+            p [:reverse,do_reverse]
+            p [:complement,do_complement]
+            p [:trim,do_trim]
+            p [:orf_reverse, orf_reverse, rec0.strand]
           end
-          seq = retval
-          if do_reverse
-            # if strand is negative, reverse
-            seq = seq.reverse if reverse
+
+          if sequence.kind_of?(Bio::FastaFormat)
+            # BioRuby conversion
+            sequence = sequence.seq
           end
-          if do_phase
-            # For forward strand features, phase is counted from the start
-            # field. For reverse strand features, phase is counted from the end
-            # field. 
-            #
-            # With a reverse protein coding string in Wormbase 
-            # the phase appears to be disregarded - or rather handled 
-            # by start-stop. This is a hack.
-            if do_reverse and reverse and (seq.size % 3 == 0)
-              # do nothing
-            else
-              seq = seq[frame..-1] if frame != 0 # set phase
+          # Generate array of sequences
+          seq = sectionlist.map { | section |
+            rec = section.rec
+            s = sequence[(section.begin-1)..(section.end-1)]
+            if do_reverse and orf_reverse
+              s = s.reverse 
             end
-          end
-          if do_complement
-            # if strand is negative, forward complement
-            if reverse
-              ntseq = Bio::Sequence::NA.new(seq)
-              seq = ntseq.forward_complement.upcase
+            # Correct for phase. Unfortunately the use of phase is ambiguous.
+            # Here we check whether rec.start is in line with orf_frame. If it
+            # is, we correct for phase. Otherwise it is ignored.
+            if do_phase and rec.phase
+              phase = rec.phase.to_i
+              # if ((rec.start-startpos) % 3 == 0) 
+              s = s[phase..-1]
+              # end
             end
+            s
+          }
+          # p seq
+          seq = seq.join
+          if do_complement and do_reverse and orf_reverse
+            ntseq = Bio::Sequence::NA.new(seq)
+            seq = ntseq.forward_complement.upcase
           end
           if do_trim
             reduce = seq.size % 3
@@ -279,9 +278,10 @@ module Bio
         end
 
         # Patch a sequence together from a Sequence string and an array
-        # of records and translate in the correct direction and frame
-        def assembleAA sequence, startpos, rec
-          seq = assemble(sequence, startpos, rec, :phase=>true, :reverse=>true, :complement=>true)
+        # 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 }
+          seq = assemble(sequence, startpos, reclist, options)
           ntseq = Bio::Sequence::NA.new(seq)
           ntseq.translate
         end

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

@@ -58,7 +58,7 @@ module Bio
        end
 
       def fasta_rec header, buf
-        fst = Bio::FastaFormat.new(header+"\n"+buf.to_s)
+        fst = Bio::FastaFormat.new(header+"\n"+buf.join(''))
         return fst.definition, fst
       end
 

data/spec/gff3_assemble2_spec.rb

@@ -6,7 +6,7 @@
 #
 $: << "../lib"
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
 include Bio::GFFbrowser
 

data/spec/gff3_assemble3_spec.rb

@@ -1,12 +1,12 @@
 # RSpec for BioRuby-GFF3-Plugin. Run with something like:
 #
-#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_assemble3_spec.rb 
+#   rspec -I ../bioruby/lib/ spec/gff3_assemble3_spec.rb 
 #
-# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+# Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>
 #
 $: << "../lib"
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
 include Bio::GFFbrowser
 

data/spec/gff3_assemble_spec.rb

@@ -1,12 +1,12 @@
 # RSpec for BioRuby-GFF3-Plugin. Run with something like:
 #
-#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_assemble_spec.rb 
+#   rspec -I ../bioruby/lib/ spec/gff3_assemble_spec.rb 
 #
-# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+# Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>
 #
 $: << "../lib"
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
 include Bio::GFFbrowser
 
@@ -83,17 +83,20 @@ describe GFFdb, "Assemble CDS" do
     aaseq = @gff.assembleAA(@contigsequence,component.start,[cds0])
     aaseq.should == "MRPLTDEETEKFFKKLSNYIGDNIKLLLEREDGEYVFRLHKDRVYYC"
   end
+  # MhA1_Contig1133	WormBase	CDS	8065	8308	.	+	1	ID=cds:MhA1_Contig1133.frz3.gene4;Parent=transcript:MhA1_Contig1133.frz3.gene4
   it "should translate CDS 8065:8308 (in frame 1, + strand)" 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], :phase => false)
+    seq = @gff.assemble(@contigsequence,component.start,[cds1])
     seq.size.should == 244
     seq.should == "TGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
-    seq = @gff.assemble(@contigsequence,component.start,[cds1])
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase => true)
+    seq.size.should == 243
     seq.should == "GAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
-    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1])
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1],:phase => true) 
     # note it should handle the frame shift and direction!
+    # wormbase validated
     aaseq.should == "EKLMRQAACIGRKQLGSFGTCLGKFTKGGSFFLHITSLDYLAPYALAKIWLKPQAEQQFLYGNNIVKSGVGRMSEGIEEKQ"
   end
   it "should translate CDS3 (in frame 0, + strand)" do
@@ -114,7 +117,7 @@ describe GFFdb, "Assemble CDS" do
     seq.size.should == 543
     seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAGTGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAAGGTATTATTATTTATAATATGTCAGATTTACCATTGGGTTTTGGAGTGGCTGCAAAGGGAACATTATCTTGTAGAAAAGTAGATCCTACAGCTTTAGTTGTTTTACATCAATCAGATTTGGGTGAATATATTCGAAATGAAGAGGGATTAATTTAA"
     seq = @gff.assemble(@contigsequence,component.start,recs)
-    seq.size.should == 543
+    seq.size.should == 543 # auto correct for phase problem
     seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAGTGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAAGGTATTATTATTTATAATATGTCAGATTTACCATTGGGTTTTGGAGTGGCTGCAAAGGGAACATTATCTTGTAGAAAAGTAGATCCTACAGCTTTAGTTGTTTTACATCAATCAGATTTGGGTGAATATATTCGAAATGAAGAGGGATTAATTTAA"
     aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
     aaseq.should == "MRPLTDEETEKFFKKLSNYIGDNIKLLLEREDGEYVFRLHKDRVYYCSEKLMRQAACIGRKQLGSFGTCLGKFTKGGSFFLHITSLDYLAPYALAKIWLKPQAEQQFLYGNNIVKSGVGRMSEGIEEKQGIIIYNMSDLPLGFGVAAKGTLSCRKVDPTALVVLHQSDLGEYIRNEEGLI*"
@@ -161,17 +164,17 @@ describe GFFdb, "Assemble CDS" do
     # tctttgtgcttccaaacgagctaatgacattccactacgatctcgcaatgattgtcgtct
     # aattgcacctctagctgagaaaggattttctaatgttgaaggtggttgttgaggagattc
     # aaacttttttctt
-    cds1 = recs[5]
-    cds1.start.should == 27981
-    cds1.frame.should == 1
-    cds1.strand.should == '-'
-    seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase=>true,:reverse=>true)
+    cds5 = recs[5]
+    cds5.start.should == 27981
+    cds5.frame.should == 1
+    cds5.strand.should == '-'
+    seq = @gff.assemble(@contigsequence,component.start,[cds5],:phase=>true,:complement=>false)
     seq.should == "TCTTTTTTCAAACTTAGAGGAGTTGTTGGTGGAAGTTGTAATCTTTTAGGAAAGAGTCGATCTCCACGTTAATCTGCTGTTAGTAACGCTCTAGCATCACCTTACAGTAATCGAGCAAACCTTCGTGTTTCTCTCCCAAGACTGGAATAATCTTCAATATTATCATTTCTTCTGGAAAGAAGATTATGTCGC"
     seq.size.should == 192
-    seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase=>true,:reverse=>true,:complement=>true)
+    seq = @gff.assemble(@contigsequence,component.start,[cds5],:phase=>true,:reverse=>true,:complement=>true)
     seq.should == "AGAAAAAAGTTTGAATCTCCTCAACAACCACCTTCAACATTAGAAAATCCTTTCTCAGCTAGAGGTGCAATTAGACGACAATCATTGCGAGATCGTAGTGGAATGTCATTAGCTCGTTTGGAAGCACAAAGAGAGGGTTCTGACCTTATTAGAAGTTATAATAGTAAAGAAGACCTTTCTTCTAATACAGCG"
     seq.size.should == 192
-    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1])
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds5],:phase=>true)
     # note it should handle the frame shift and direction!
     # >EMBOSS_001_4
     # RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA
@@ -190,9 +193,9 @@ describe GFFdb, "Assemble CDS" do
     cds2.start.should == 27981
     cds2.frame.should == 1
     cds2.strand.should == '-'
-    seq = @gff.assemble(@contigsequence,component.start,[cds2],:complement=>true)
-    seq.should == "GCGACATAATCTTCTTTCCAGAAGAAATGATAATATTGAAGATTATTCCAGTCTTGGGAGAGAAACACGAAGGTTTGCTCGATTACTGTAAGGTGATGCTAGAGCGTTACTAACAGCAGATTAACGTGGAGATCGACTCTTTCCTAAAAGATTACAACTTCCACCAACAACTCCTCTAAGTTTGAAAAAAGAA"
-    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2])
+    seq = @gff.assemble(@contigsequence,component.start,[cds2],:reverse=>false,:complement=>true)
+    seq.should == "CGCTGTATTAGAAGAAAGGTCTTCTTTACTATTATAACTTCTAATAAGGTCAGAACCCTCTCTTTGTGCTTCCAAACGAGCTAATGACATTCCACTACGATCTCGCAATGATTGTCGTCTAATTGCACCTCTAGCTGAGAAAGGATTTTCTAATGTTGAAGGTGGTTGTTGAGGAGATTCAAACTTTTTTCT"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2],:phase=>true)
     # note it should handle the frame shift and direction!
     # >27981..28173_4 RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA
     aaseq.should == "RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA"
@@ -222,17 +225,17 @@ describe GFFdb, "Assemble CDS" do
     cds2.strand.should == '-'
     seq = @gff.assemble(@contigsequence,component.start,[cds2], :raw=>true)
     seq.should == "ATAAATTTCCCTTTCTCCAGAAAAACTTACAAAAGTAGATTTATCAACAGAATTTCTTTGATCTAAAGGTAATCCTCTTTGATGTAAAATTTTCATATCATTTAACATTTCCCTTTCTGGTTGTTGTCTTCTTTCATCAATCATTTCTTGTGTAATTCCTCTAGCAGCCATTTCAGATTCAATAAGGTCAAGGGTTTGTTCATCATCACAAATATCATAAGGCATATTACCATCTGCATTTACTGCTAGTAAATCTGCGTTG"
-    seq = @gff.assemble(@contigsequence,component.start,[cds2], :codonize=>true)
+    seq = @gff.assemble(@contigsequence,component.start,[cds2], :phase=>true)
     seq.should == "AACGCAGATTTACTAGCAGTAAATGCAGATGGTAATATGCCTTATGATATTTGTGATGATGAACAAACCCTTGACCTTATTGAATCTGAAATGGCTGCTAGAGGAATTACACAAGAAATGATTGATGAAAGAAGACAACAACCAGAAAGGGAAATGTTAAATGATATGAAAATTTTACATCAAAGAGGATTACCTTTAGATCAAAGAAATTCTGTTGATAAATCTACTTTTGTAAGTTTTTCTGGAGAAAGGGAAATTTAT"
     # cds1.frame = 1
-    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2])
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2],:phase=>true)
     # note it should handle the frame shift and direction!
     aaseq.should == "NADLLAVNADGNMPYDICDDEQTLDLIESEMAARGITQEMIDERRQQPEREMLNDMKILHQRGLPLDQRNSVDKSTFVSFSGEREIY"
   end
   it "should assemble the protein sequence for MhA1_Contig1133.frz3.gene11" do
     recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
     component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
-    seq = @gff.assemble(@contigsequence,component.start,recs, :phase=>true, :reverse=>true, :complement=>true)
+    seq = @gff.assemble(@contigsequence,component.start,recs, :reverse=>true, :complement=>true)
     seq.should == "ATGGACCATCATGCATTGGTGGAGGAATTACCAGAAATTGAAAAATTAACTCCTCAAGAACGTATTGCATTAGCTAGAGAACGCCGTGCTGAACAACTTCGACAGAATGCTGCACGGGAGGCTCAATTGCCAATGCCTGCACAGCGCCGGCCTCGTCTTCGATTTACACCAGATGTTGCTTTACTTGAGGCAACATGTGCCATTGACAATAATGAAAGAATTGTTCGTCTTCTGCTTAGGTACGGAGCTTGTGTTAATGCCAAAGACACTGAACTTTGGACACCATTGCACGCAGCTGCATGTTGTGCTTATATTGATATTGTTCGATTGCTTATTGCACACAACGCAGATTTACTAGCAGTAAATGCAGATGGTAATATGCCTTATGATATTTGTGATGATGAACAAACCCTTGACCTTATTGAATCTGAAATGGCTGCTAGAGGAATTACACAAGAAATGATTGATGAAAGAAGACAACAACCAGAAAGGGAAATGTTAAATGATATGAAAATTTTACATCAAAGAGGATTACCTTTAGATCAAAGAAATTCTGTTGATAAATCTACTTTTGTAAGTTTTTCTGGAGAAAGGGAAATTTATTTACATATAGCAGCAGCTAATGGTTATTATGATGTTGCTGCTTTCCTTCTTCGTTGTAATGTTTCTCCAGCATTGAGAGATATAGATTTGTGGCAACCAATTCATGCAGCTGCTTCTTGGAATCAACCAGACTTAATCGAGCTTTTATGCGAATATGGGGCTGATATAAATGCAAAAACTGGAGCTGGGGAAAGCCCTTTAGAATTAACTGAAGATGAACCAACCCAACAAGTAATTAGAACAATCGCTCAGACAGAAGCAAGGAGACGGCGTGGTCCAGGTGGTGGTTACTTTGGTGTTCGTGATTCTCGACGACAAAGCCGAAAAAGAAAAAAGTTTGAATCTCCTCAACAACCACCTTCAACATTAGAAAATCCTTTCTCAGCTAGAGGTGCAATTAGACGACAATCATTGCGAGATCGTAGTGGAATGTCATTAGCTCGTTTGGAAGCACAAAGAGAGGGTTCTGACCTTATTAGAAGTTATAATAGTAAAGAAGACCTTTCTTCTAATACAGCGGATGATTCTTTAAATGTTGGAAGTTCTTCATATCTCAACAATCCAACAGCCTCGGCTAGTGCTTCCTCTTCAGCATTACACGGAACTCCACATCAACAACAACGTCGTGAATCTCCACCTAAACGTGCATTAATGGCTAGAAGTGCTTCTCATCAAAAACAAAAACAACAAATGTCTCCAGATGAATGGCTGAAAAAATTAGAAGCAGATTCTGCAGGTTTTCGAGATAATGATGGAGAAGATGGTGAATTACAATCTGAACTTAAAGGAGGACAAAGAATGAAGAGTGGTGGTGGTGGAGGAGCGAGAGGTCAGCAAGAAATGAATGGTGGTCCAACAGCAACATTTGGTGGAGCTTCAAAACAACAATTAGCAATGGGCTCTGGACCCAATAGACGGCGCAAACAAGGATGTTGCTCTGTTTTGTGA"
     aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
     aaseq.should == "MDHHALVEELPEIEKLTPQERIALARERRAEQLRQNAAREAQLPMPAQRRPRLRFTPDVALLEATCAIDNNERIVRLLLRYGACVNAKDTELWTPLHAAACCAYIDIVRLLIAHNADLLAVNADGNMPYDICDDEQTLDLIESEMAARGITQEMIDERRQQPEREMLNDMKILHQRGLPLDQRNSVDKSTFVSFSGEREIYLHIAAANGYYDVAAFLLRCNVSPALRDIDLWQPIHAAASWNQPDLIELLCEYGADINAKTGAGESPLELTEDEPTQQVIRTIAQTEARRRRGPGGGYFGVRDSRRQSRKRKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTADDSLNVGSSSYLNNPTASASASSSALHGTPHQQQRRESPPKRALMARSASHQKQKQQMSPDEWLKKLEADSAGFRDNDGEDGELQSELKGGQRMKSGGGGGARGQQEMNGGPTATFGGASKQQLAMGSGPNRRRKQGCCSVL*"

data/spec/gff3_fileiterator_spec.rb

@@ -1,12 +1,12 @@
 # RSpec for BioRuby-GFF3-Plugin. Run with something like:
 #
-#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_spec.rb 
+#   rspec -I ../bioruby/lib/ spec/gff3_fileiterator_spec.rb 
 #
 # Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
 #
 $: << "../lib"
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
 TEST1='test/data/gff/test.gff3'
 TEST2='test/data/gff/standard.gff3'

data/spec/gffdb_spec.rb

@@ -1,13 +1,13 @@
 # RSpec for BioRuby-GFF3-Plugin. Run with something like:
 #
-#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gffdb_spec.rb 
+#   rspec -I ../bioruby/lib/ spec/gffdb_spec.rb 
 #
 # Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
 #
 $: << "../lib"
 
 
-require 'bio/db/gff/gffdb'
+require 'bio-gff3'
 
 include Bio::GFFbrowser
 

data/test/data/gff/test.gff3

@@ -64,11 +64,11 @@ AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
 GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
 CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
 >test02
-ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
+ACGACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
 GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
 CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
 AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
 GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
-CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
+CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGACAAAAAA
 
 

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 6
+  - 8
   - 0
-  version: 0.6.0
+  version: 0.8.0
 platform: ruby
 authors: 
 - Pjotr Prins
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-12-29 00:00:00 +01:00
+date: 2010-12-31 00:00:00 +01:00
 default_executable: gff3-fetch
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -88,6 +88,19 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id006
 description: |
   GFF3 (genome browser) information and digest mRNA and CDS sequences.
   Options for low memory use and caching of records.
@@ -100,13 +113,11 @@ extensions: []
 
 extra_rdoc_files: 
 - LICENSE.txt
-- README
 - README.rdoc
 files: 
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
-- README
 - README.rdoc
 - Rakefile
 - VERSION
@@ -151,7 +162,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -266764915
+      hash: -1033924243
       segments: 
       - 0
       version: "0"

data/README

@@ -1,65 +0,0 @@
-= GFF3 plugin for BioRuby, aimed at parsing big data =
-
-Features:
-
-# Take GFF (genome browser) information and digest mRNA and CDS sequences
-# Options for low memory use and caching of records
-# Support for external FASTA files
-
-You can use this plugin in two ways. First as a standalone program, next as a
-plugin library to BioRuby.
-
-For example, fetch mRNA and CDS information from GFF3 files and output to FASTA:
-
-  ./bin/gff3-fetch mrna test/data/gff/test.gff3
-  ./bin/gff3-fetch cds test/data/gff/test.gff3
-
-Or clone this repository and add the 'lib' dir to the Ruby search path and 
-
-  require 'bio/db/gff/gffdb'
-
-You can also run RSpec with something like
-
-   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gffdb_spec.rb
-
-This implementation depends on BioRuby's basic GFF3 parser, with the possible
-advantage that the plugin is faster and does not consume all memory. The Gff3
-specs are based on the output of the Wormbase genome browser.
-
-For a write-up see http://thebird.nl/bioruby/BioRuby_GFF3.html 
-
-Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl> 
-
--------------------------------------------------------------------------------
-
-Usage:
-
-BioRuby GFF3 Plugin Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
-
-  Fetch and assemble mRNAs, or CDS and print in FASTA format. 
-
-    gff3-fetch [--no-cache] mRNA|CDS [filename.fa] filename.gff
-
-  Where:
-
-    --no-cache      : do not load everything in memory 
-    mRNA            : assemble mRNA
-    CDS             : assemble CDS 
-
-  Multiple GFF3 files can be used. For external FASTA files, always the last
-  one before the GFF file is used.
-
-  Examples:
-
-    Find mRNA and CDS information from test.gff3 (which includes sequence information)
-
-      ./bin/gff3-fetch mRNA test/data/gff/test.gff3
-      ./bin/gff3-fetch CDS test/data/gff/test.gff3
-
-    Find mRNA from external FASTA file, without loading everythin in RAM
-
-      ./bin/gff3-fetch --no-cache mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
-
-  If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
-
-