bio-gff3 0.8.3 → 0.8.4

data/README.rdoc

@@ -58,3 +58,91 @@ For a write-up see http://thebird.nl/bioruby/BioRuby_GFF3.html
 Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl> 
 
 
+
+  Fetch and assemble GFF3 types (e.g. ORF, mRNA, CDS) + print in FASTA format. 
+
+    gff3-fetch [--low-mem] [--validate] type [filename.fa] filename.gff3
+
+  Where (NYI == Not Yet Implemented):
+
+    --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
+  
+  type is any valid type in the GFF3 definition. For example:
+
+    mRNA            : assemble mRNA
+    CDS             : assemble CDS 
+    exon            : list all exons
+    gene|ORF        : list gene ORFs 
+    other           : use any type from GFF3 definition, e.g. 'Terminate' -- NYI
+
+  and the following performance options:
+
+    --cache full    : load all in RAM (fast)
+    --cache none    : do not load anything in memory (slow)
+    --low-mem       : use LRU cache (limit RAM use, fast) -- NYI
+    --max-cpus num  : use num threads -- NYI
+    --emboss        : use EMBOSS translation (fast) -- NYI
+
+  Multiple GFF3 files can be used. With external FASTA files, always the last
+  one before the GFF3 filename is matched.
+
+  Note that above switches are only partially implemented at this stage. Full
+  feature support is projected Feb. 2011.
+
+  Examples:
+
+    Assemble 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 records from external FASTA file, adding phase and translate to protein sequence
+
+      gff3-fetch --no-assemble --add-phase --translate 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 --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+      gff3-fetch --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+
+    Validate GFF3 file using EMBOSS translation and validation
+
+      gff3-fetch --cache none --validate --emboss mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+
+    Find GENEID predicted terminal exons
+
+      gff3-fetch terminal chromosome1.fa geneid.gff3
+
+== Performance
+
+time gff3-fetch cds m_hapla.WS217.dna.fa m_hapla.WS217.gff3 > test.fa
+
+  Cache      real     user     sys
+  ----------------------------------------------------
+  full       12m41s   12m28s   0m09s (0.8.0 Jan. 2011)
+  none      504m39s  477m49s  26m50s (0.8.0 Jan. 2011)
+  ----------------------------------------------------
+
+where
+
+   52M m_hapla.WS217.dna.fa
+  456M m_hapla.WS217.gff3
+
+ruby 1.9.2p136 (2010-12-25 revision 30365) [x86_64-linux]
+on an 8 CPU, 2.6 GHz (6MB cache), 16 GB RAM machine. 
+
+== Cite
+
+  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> 
+

data/VERSION

@@ -1 +1 @@
-0.8.3
+0.8.4

data/bin/gff3-fetch

@@ -26,7 +26,7 @@ USAGE = <<EOM
     mRNA            : assemble mRNA
     CDS             : assemble CDS 
     exon            : list all exons
-    gene/ORF        : list gene ORFs -- NYI
+    gene|ORF        : list gene ORFs 
     other           : use any type from GFF3 definition, e.g. 'Terminate' -- NYI
 
   and the following performance options:
@@ -167,8 +167,6 @@ opts.parse!(ARGV)
 
 gfftype = ARGV.shift
 
-raise "Unknown GFF type '#{gfftype}'" if gfftype !~ /mrna|cds|exon/i
-
 fastafn = nil
 
 ARGV.each do | fn |
@@ -189,7 +187,15 @@ ARGV.each do | fn |
   gff = gffdb.assembler
   writer = Bio::GFFbrowser::FastaWriter.new(options.translate, options.validate)
   case gfftype.downcase
-    when 'mrna' 
+    when 'gene'
+          gff.each_gene_seq do | id, seq |
+            writer.put(id,seq)
+          end
+    when 'orf'
+          gff.each_gene_seq do | id, seq |
+            writer.put(id,seq)
+          end
+    when 'mrna'
           gff.each_mRNA_seq do | id, seq |
             writer.put(id,seq)
           end
@@ -202,7 +208,7 @@ ARGV.each do | fn |
             writer.put(id,seq)
           end
     else
-      raise "Unknown action <#{gfftype}>"
+      raise "Unknown action on type <#{gfftype}>"
   end
   fastafn = nil
 end

data/bio-gff3.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gff3}
-  s.version = "0.8.3"
+  s.version = "0.8.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]

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

@@ -30,6 +30,7 @@ module Bio
           @count_ids          = Counter.new   # Count ids
           @count_seqnames     = Counter.new   # Count seqnames
           @componentlist      = {} # Store containers, like genes, contigs
+          @orflist            = LinkedRecs.new
           @mrnalist           = LinkedRecs.new   # Store linked mRNA records
           @cdslist            = LinkedRecs.new
           @exonlist           = LinkedRecs.new

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

@@ -90,6 +90,7 @@ module Bio
           @count_ids          = Counter.new   # Count ids
           @count_seqnames     = Counter.new   # Count seqnames
           @componentlist      = SeekRecList.new(@iter.fh) # Store containers, like genes, contigs
+          @orflist            = SeekLinkedRecs.new   # Store linked gene records
           @mrnalist           = SeekLinkedRecs.new   # Store linked mRNA records
           @cdslist            = SeekLinkedRecs.new
           @exonlist           = SeekLinkedRecs.new

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

@@ -23,24 +23,26 @@ module Bio
             @count_ids.add(id)
             @count_seqnames.add(rec.seqname)
 
-            if COMPONENT_TYPES.include?(rec.feature_type)
+            is_component = COMPONENT_TYPES.include?(rec.feature_type)
+            if is_component
               # check for container ID
               warn("Container <#{rec.feature_type}> has no ID, so using sequence name instead",id) if rec.id == nil
               @componentlist[id] = rec
               info "Added #{rec.feature_type} with component ID #{id}"
-            else
-              case rec.feature_type
-                when 'mRNA' || 'SO:0000234'
-                  @mrnalist.add(id,rec)
-                when 'CDS'  || 'SO:0000316'
-                  @cdslist.add(id,rec)
-                when 'exon' || 'SO:0000147'
-                  @exonlist.add(id,rec)
-                else
-                  if !IGNORE_FEATURES.include?(rec.feature_type)
-                    @unrecognized_features[rec.feature_type] = true
-                  end
-              end
+            end 
+            case rec.feature_type
+              when 'gene' || 'SO:0000704'
+                @orflist.add(id,rec)
+              when 'mRNA' || 'SO:0000234'
+                @mrnalist.add(id,rec)
+              when 'CDS'  || 'SO:0000316'
+                @cdslist.add(id,rec)
+              when 'exon' || 'SO:0000147'
+                @exonlist.add(id,rec)
+              else
+                if !is_component and !IGNORE_FEATURES.include?(rec.feature_type)
+                  @unrecognized_features[rec.feature_type] = true
+                end
             end
         end
 
@@ -80,6 +82,12 @@ module Bio
           # p :inmemory, @sequencelist
         end
 
+        # Yield the id, recs, containing component and sequence of genes
+        def each_gene
+          parse if !@orflist
+          each_item(@orflist) { |id, recs, component | yield id, recs, component }
+        end
+
         # Yield the id, recs, containing component and sequence of mRNAs
         def each_mRNA
           parse if !@mrnalist
@@ -98,6 +106,21 @@ module Bio
           each_item(@exonlist) { |id, recs, component | yield id, recs, component }
         end
 
+        # Yield a unique description and the sequence
+        def each_gene_seq
+          each_gene do | id, reclist, component |
+            if component
+              sequence = @sequencelist[component.seqname]
+              # p sequence
+              if sequence
+                yield description(id,component,reclist), assemble(sequence,component.start,reclist)
+              else 
+                error "No sequence information for",id
+              end
+            end
+          end
+        end
+
         # Yield a unique description and the sequence
         def each_mRNA_seq
           each_mRNA do | id, reclist, component |

data/spec/gff3_fileiterator_spec.rb

@@ -29,7 +29,7 @@ describe Bio::GFF::GFF3::FileIterator, "iterates a GFF3 file" do
       # p [id, rec]
       last = rec
     end
-    last.io_seek.should == 3256
+    last.io_seek.should == 3342
     firstid = 'unknown'
     iter.each_sequence do | id, seq |
       # p [id, seq]

data/spec/gffdb_spec.rb

@@ -22,13 +22,15 @@ TESTGFF1FASTA='test/data/gff/test-ext-fasta.fa'
 def iterators_should_be_implemented
   if TEST_NON_IMPLEMENTED
     it "should implement each_gene" 
-    it "should implement each_gene" 
-    it "should implement each_gene_seq" 
     it "should implement each_mRNA" 
     it "should implement each_exon" 
     it "should implement each_exon_seq" 
     it "should implement each_CDS" 
   end
+  it "should implement each_gene_seq" do
+    h = {} ; @gff.each_gene_seq { | id, seq | h[id] = seq }
+    h["gene01 Sequence:test01_1:400 (3:280)"].should == "GAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTAGTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTA" if h["gene01 Sequence:test01_1:400 (3:280)"]
+  end
   it "should implement each_mRNA_seq" do
     h = {} ; @gff.each_mRNA_seq { | id, seq | h[id] = seq }
     h["mrna01short Sequence:test01_1:400 (3:14)"].should == "GAAGATTTGTAT"

data/test/data/gff/test.gff3

@@ -44,6 +44,7 @@ Contig4	confirmed	CDS	32000	35000	.	+	.	ID=Misc:thing3;mRNA=trans-9
 ##gff-version 3
 ##sequence-region test01 1 400
 test01	RANDOM	contig	1	400	.	+	.	ID=test01;Note=this is test
+test01	.	gene	3	280	.	+	.	ID=gene01;Name=tesGene;Parent=test01;Note=this is test gene
 test01	.	mRNA	3	14	.	+	.	ID=mrna01short;Name=testmRNA;Note=this is test mRNA
 test01	.	mRNA	101	230	.	+	.	ID=mrna01;Name=testmRNA;Note=this is test mRNA
 test01	.	mRNA	101	280	.	+	.	ID=mrna01a;Name=testmRNAalterative;Note=test of alternative splicing variant

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 8
-  - 3
-  version: 0.8.3
+  - 4
+  version: 0.8.4
 platform: ruby
 authors: 
 - Pjotr Prins
@@ -180,7 +180,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -450771567
+      hash: 520620943
       segments: 
       - 0
       version: "0"