bio-gff3 0.8.5 → 0.8.6

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Files changed (30) hide show
  1. data/Gemfile +3 -2
  2. data/Rakefile +13 -4
  3. data/VERSION +1 -1
  4. data/bin/gff3-fetch +50 -14
  5. data/bio-gff3.gemspec +15 -20
  6. data/lib/bio/db/gff/block/gffblockparser.rb +93 -0
  7. data/lib/bio/db/gff/digest/gffinmemory.rb +2 -0
  8. data/lib/bio/db/gff/digest/gfflrucache.rb +208 -0
  9. data/lib/bio/db/gff/digest/gffnocache.rb +28 -9
  10. data/lib/bio/db/gff/digest/gffparser.rb +1 -1
  11. data/lib/bio/db/gff/file/gfffileiterator.rb +16 -7
  12. data/lib/bio/db/gff/gff3.rb +15 -5
  13. data/lib/bio/db/gff/gff3parserec.rb +1 -6
  14. data/lib/bio/db/gff/gffcomponent.rb +8 -6
  15. data/lib/bio/db/gff/gffrecord.rb +13 -8
  16. data/lib/bio/db/gff/gffsection.rb +0 -1
  17. data/lib/bio/db/gff/gffsequence.rb +3 -9
  18. data/lib/bio/db/gff/gffvalidate.rb +1 -1
  19. data/lib/bio/output/gfflogger.rb +10 -1
  20. data/spec/gff3_fileiterator_spec.rb +5 -4
  21. data/spec/gffdb_spec.rb +7 -1
  22. data/spec/gffparserec.rb +1 -1
  23. data/test/data/regression/test_ext_gff3.rtest +4 -5
  24. data/test/data/regression/test_gff3.rtest +4 -5
  25. data/test/data/regression/test_lrucache_ext_gff3.rtest +64 -0
  26. data/test/data/regression/test_lrucache_gff3.rtest +68 -0
  27. data/test/data/regression/test_nocache_ext_gff3.rtest +2 -0
  28. data/test/data/regression/test_nocache_gff3.rtest +3 -6
  29. data/test/test_bio-gff3.rb +6 -1
  30. metadata +37 -77
data/spec/gffparserec.rb CHANGED
@@ -23,7 +23,7 @@ describe FastLineParser, "GFF3 Fast line parser" do
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  parse_attributes_fast("id=1%3Bparent=45").should == { "id"=>"1%3Bparent=45" }
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  end
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  it "should parse records" do
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- parse_line_fast("ctg123\t.\tCDS\t1201\t1500\t.\t+\t0\tID=cds00001;Parent=mRNA00001;Name=edenprotein.1").should == ["ctg123", ".", "CDS", 1201, 1500, 0.0, "+", 0, {"ID"=>"cds00001", "Parent"=>"mRNA00001", "Name"=>"edenprotein.1"}]
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+ parse_line_fast("ctg123\t.\tCDS\t1201\t1500\t.\t+\t0\tID=cds00001;Parent=mRNA00001;Name=edenprotein.1").should == ["ctg123", ".", "CDS", "1201", "1500", ".", "+", "0", "ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"]
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  end
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  it "should handle a Record interface" do
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  fields =
data/test/data/regression/test_ext_gff3.rtest CHANGED
@@ -1,3 +1,4 @@
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+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
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  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
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  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -10,7 +11,6 @@
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 1 2000>
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  INFO bio-gff3: Added Component with component ID Contig2 1 2000 <>
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  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 5000>
@@ -21,20 +21,16 @@
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  INFO bio-gff3: Added Component with component ID Contig2 2001 37450 <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-3 <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-4 <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added Component with component ID Clone:AL12345.2 <>
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  INFO bio-gff3: Adding mRNA <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added Component with component ID Clone:ABC123 <>
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  INFO bio-gff3: Added gene with component ID Misc:thing1 <>
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  INFO bio-gff3: Adding gene <Misc:thing1> <>
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  INFO bio-gff3: Adding mRNA <Misc:thing2> <>
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  INFO bio-gff3: Adding CDS <Misc:thing3> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added contig with component ID test01 <>
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  INFO bio-gff3: Adding mRNA <mrna01short> <>
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  INFO bio-gff3: Adding mRNA <mrna01> <>
@@ -46,6 +42,8 @@
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  INFO bio-gff3: Adding CDS <cds1> <>
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  INFO bio-gff3: Adding CDS <cds1> <>
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  INFO bio-gff3: Adding CDS <cds2> <>
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+ INFO bio-gff3: Memory used After reading GFF RAM 10M, VMEM 14M
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+ INFO bio-gff3: Memory used After reading FASTA RAM 10M, VMEM 14M
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  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
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  WARN bio-gff3: No sequence information for <mRNA:trans-8>
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  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:ABC123>
@@ -59,3 +57,4 @@ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGA
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  INFO bio-gff3: find_component: Matched seqname <test01>
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  >mrna01a Sequence:test01_1:400 (101:280)
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  TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
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+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/data/regression/test_gff3.rtest CHANGED
@@ -1,3 +1,4 @@
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+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
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  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
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  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -10,7 +11,6 @@
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 1 2000>
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  INFO bio-gff3: Added Component with component ID Contig2 1 2000 <>
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  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 5000>
@@ -21,20 +21,16 @@
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  INFO bio-gff3: Added Component with component ID Contig2 2001 37450 <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-3 <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-4 <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added Component with component ID Clone:AL12345.2 <>
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  INFO bio-gff3: Adding mRNA <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added Component with component ID Clone:ABC123 <>
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  INFO bio-gff3: Added gene with component ID Misc:thing1 <>
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  INFO bio-gff3: Adding gene <Misc:thing1> <>
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  INFO bio-gff3: Adding mRNA <Misc:thing2> <>
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  INFO bio-gff3: Adding CDS <Misc:thing3> <>
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- WARN bio-gff3: Record with unknown ID. . . . . . . . .
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  INFO bio-gff3: Added contig with component ID test01 <>
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  INFO bio-gff3: Added gene with component ID gene01 <>
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  INFO bio-gff3: Adding gene <gene01> <>
@@ -48,6 +44,8 @@
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  INFO bio-gff3: Adding CDS <cds1> <>
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  INFO bio-gff3: Adding CDS <cds1> <>
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  INFO bio-gff3: Adding CDS <cds2> <>
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+ INFO bio-gff3: Memory used After reading GFF RAM 10M, VMEM 14M
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+ INFO bio-gff3: Memory used After reading FASTA RAM 10M, VMEM 14M
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  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Transcript:trans-1>
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  WARN bio-gff3: No sequence information for <Transcript:trans-1>
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  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
@@ -63,3 +61,4 @@ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
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  INFO bio-gff3: find_component: Matched seqname <test01>
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  >cds2 Sequence:test01_1:400 (192:200)
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  TTCATGGGC
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+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/data/regression/test_lrucache_ext_gff3.rtest ADDED
@@ -0,0 +1,64 @@
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+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
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+ INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-2 <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 1 2000>
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+ INFO bio-gff3: Added Component with component ID Contig2 1 2000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 5000>
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+ INFO bio-gff3: Added Component with component ID Contig2 2001 5000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 5001 20000>
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+ INFO bio-gff3: Added Component with component ID Contig2 5001 20000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 37450>
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+ INFO bio-gff3: Added Component with component ID Contig2 2001 37450 <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-3 <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-4 <>
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+ INFO bio-gff3: Added Component with component ID Clone:AL12345.2 <>
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+ INFO bio-gff3: Adding mRNA <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Added Component with component ID Clone:ABC123 <>
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+ INFO bio-gff3: Added gene with component ID Misc:thing1 <>
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+ INFO bio-gff3: Adding gene <Misc:thing1> <>
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+ INFO bio-gff3: Adding mRNA <Misc:thing2> <>
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+ INFO bio-gff3: Adding CDS <Misc:thing3> <>
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+ INFO bio-gff3: Added contig with component ID test01 <>
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+ INFO bio-gff3: Adding mRNA <mrna01short> <>
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+ INFO bio-gff3: Adding mRNA <mrna01> <>
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+ INFO bio-gff3: Adding mRNA <mrna01a> <>
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+ INFO bio-gff3: Adding exon <exon01> <>
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+ INFO bio-gff3: Adding exon <exon02> <>
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+ INFO bio-gff3: Adding exon <exon02a> <>
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+ INFO bio-gff3: Adding CDS <cds_short> <>
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+ INFO bio-gff3: Adding CDS <cds1> <>
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+ INFO bio-gff3: Adding CDS <cds1> <>
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+ INFO bio-gff3: Adding CDS <cds2> <>
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+ INFO bio-gff3: Cache calls After reading files = 0 <>
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+ INFO bio-gff3: Cache hits After reading files = 0 <>
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+ INFO bio-gff3: Cache misses After reading files = 0 <>
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+ INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
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+ WARN bio-gff3: No sequence information for <mRNA:trans-8>
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+ INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:ABC123>
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+ WARN bio-gff3: No sequence information for <Misc:thing2>
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >mrna01short Sequence:test01_1:400 (3:14)
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+ GAAGATTTGTAT
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >mrna01 Sequence:test01_1:400 (101:230)
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+ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTC
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >mrna01a Sequence:test01_1:400 (101:280)
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+ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
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+ INFO bio-gff3: Cache calls After iterating = 54 <>
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+ INFO bio-gff3: Cache hits After iterating = 37 <>
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+ INFO bio-gff3: Cache misses After iterating = 17 <>
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+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/data/regression/test_lrucache_gff3.rtest ADDED
@@ -0,0 +1,68 @@
1
+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
2
+ INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
3
+ INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Adding CDS <Transcript:trans-1> <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-2 <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ INFO bio-gff3: Adding exon <Transcript:trans-2> <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 1 2000>
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+ INFO bio-gff3: Added Component with component ID Contig2 1 2000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 5000>
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+ INFO bio-gff3: Added Component with component ID Contig2 2001 5000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 5001 20000>
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+ INFO bio-gff3: Added Component with component ID Contig2 5001 20000 <>
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+ WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 37450>
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+ INFO bio-gff3: Added Component with component ID Contig2 2001 37450 <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-3 <>
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+ INFO bio-gff3: Added transcript with component ID Transcript:trans-4 <>
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+ INFO bio-gff3: Added Component with component ID Clone:AL12345.2 <>
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+ INFO bio-gff3: Adding mRNA <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
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+ INFO bio-gff3: Added Component with component ID Clone:ABC123 <>
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+ INFO bio-gff3: Added gene with component ID Misc:thing1 <>
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+ INFO bio-gff3: Adding gene <Misc:thing1> <>
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+ INFO bio-gff3: Adding mRNA <Misc:thing2> <>
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+ INFO bio-gff3: Adding CDS <Misc:thing3> <>
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+ INFO bio-gff3: Added contig with component ID test01 <>
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+ INFO bio-gff3: Added gene with component ID gene01 <>
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+ INFO bio-gff3: Adding gene <gene01> <>
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+ INFO bio-gff3: Adding mRNA <mrna01short> <>
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+ INFO bio-gff3: Adding mRNA <mrna01> <>
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+ INFO bio-gff3: Adding mRNA <mrna01a> <>
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+ INFO bio-gff3: Adding exon <exon01> <>
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+ INFO bio-gff3: Adding exon <exon02> <>
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+ INFO bio-gff3: Adding exon <exon02a> <>
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+ INFO bio-gff3: Adding CDS <cds_short> <>
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+ INFO bio-gff3: Adding CDS <cds1> <>
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+ INFO bio-gff3: Adding CDS <cds1> <>
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+ INFO bio-gff3: Adding CDS <cds2> <>
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+ INFO bio-gff3: Cache calls After reading files = 0 <>
48
+ INFO bio-gff3: Cache hits After reading files = 0 <>
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+ INFO bio-gff3: Cache misses After reading files = 0 <>
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+ INFO bio-gff3: find_component: Matched (long search) column 0 and location <Transcript:trans-1>
51
+ WARN bio-gff3: No sequence information for <Transcript:trans-1>
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+ INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
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+ WARN bio-gff3: No sequence information for <mRNA:trans-8>
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+ INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:ABC123>
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+ WARN bio-gff3: No sequence information for <Misc:thing3>
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >cds_short Sequence:test01_1:400 (3:14)
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+ GAAGATTTGTAT
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >cds1 Sequence:test01_1:400 (164:190, 192:200)
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+ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
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+ INFO bio-gff3: find_component: Matched seqname <test01>
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+ >cds2 Sequence:test01_1:400 (192:200)
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+ TTCATGGGC
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+ INFO bio-gff3: Cache calls After iterating = 76 <>
66
+ INFO bio-gff3: Cache hits After iterating = 52 <>
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+ INFO bio-gff3: Cache misses After iterating = 24 <>
68
+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/data/regression/test_nocache_ext_gff3.rtest CHANGED
@@ -1,3 +1,4 @@
1
+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
1
2
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
2
3
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
3
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  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -54,3 +55,4 @@ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGA
54
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  INFO bio-gff3: find_component: Matched seqname <test01>
55
56
  >mrna01a Sequence:test01_1:400 (101:280)
56
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  TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
58
+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/data/regression/test_nocache_gff3.rtest CHANGED
@@ -1,4 +1,5 @@
1
- INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
1
+ INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
2
+ INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
2
3
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
3
4
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
4
5
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -10,7 +11,6 @@
10
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
11
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
12
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  INFO bio-gff3: Adding exon <Transcript:trans-2> <>
13
- WARN bio-gff3: Record with unknown ID. . . . . . . . .
14
14
  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 1 2000>
15
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  INFO bio-gff3: Added Component with component ID Contig2 1 2000 <>
16
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  WARN bio-gff3: Container <Component> has no ID, so using sequence name instead <Contig2 2001 5000>
@@ -21,20 +21,16 @@
21
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  INFO bio-gff3: Added Component with component ID Contig2 2001 37450 <>
22
22
  INFO bio-gff3: Added transcript with component ID Transcript:trans-3 <>
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  INFO bio-gff3: Added transcript with component ID Transcript:trans-4 <>
24
- WARN bio-gff3: Record with unknown ID. . . . . . . . .
25
- WARN bio-gff3: Record with unknown ID. . . . . . . . .
26
24
  INFO bio-gff3: Added Component with component ID Clone:AL12345.2 <>
27
25
  INFO bio-gff3: Adding mRNA <mRNA:trans-8> <>
28
26
  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
29
27
  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
30
28
  INFO bio-gff3: Adding CDS <mRNA:trans-8> <>
31
- WARN bio-gff3: Record with unknown ID. . . . . . . . .
32
29
  INFO bio-gff3: Added Component with component ID Clone:ABC123 <>
33
30
  INFO bio-gff3: Added gene with component ID Misc:thing1 <>
34
31
  INFO bio-gff3: Adding gene <Misc:thing1> <>
35
32
  INFO bio-gff3: Adding mRNA <Misc:thing2> <>
36
33
  INFO bio-gff3: Adding CDS <Misc:thing3> <>
37
- WARN bio-gff3: Record with unknown ID. . . . . . . . .
38
34
  INFO bio-gff3: Added contig with component ID test01 <>
39
35
  INFO bio-gff3: Added gene with component ID gene01 <>
40
36
  INFO bio-gff3: Adding gene <gene01> <>
@@ -63,3 +59,4 @@ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
63
59
  INFO bio-gff3: find_component: Matched seqname <test01>
64
60
  >cds2 Sequence:test01_1:400 (192:200)
65
61
  TTCATGGGC
62
+ INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
data/test/test_bio-gff3.rb CHANGED
@@ -20,7 +20,12 @@ class Gff3Test < Test::Unit::TestCase
20
20
 
21
21
  def test_nocache
22
22
  assert_equal(true,single_run("mRNA --cache none #{DAT}/gff/test-ext-fasta.fa #{DAT}/gff/test-ext-fasta.gff3",this_method+'_ext_gff3'))
23
- assert_equal(true,single_run("CDS #{DAT}/gff/test.gff3",this_method+'_gff3'))
23
+ assert_equal(true,single_run("CDS --cache none #{DAT}/gff/test.gff3",this_method+'_gff3'))
24
+ end
25
+
26
+ def test_lrucache
27
+ assert_equal(true,single_run("mRNA --cache lru #{DAT}/gff/test-ext-fasta.fa #{DAT}/gff/test-ext-fasta.gff3",this_method+'_ext_gff3'))
28
+ assert_equal(true,single_run("CDS --cache lru #{DAT}/gff/test.gff3",this_method+'_gff3'))
24
29
  end
25
30
 
26
31
  private
metadata CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
5
5
  segments:
6
6
  - 0
7
7
  - 8
8
- - 5
9
- version: 0.8.5
8
+ - 6
9
+ version: 0.8.6
10
10
  platform: ruby
11
11
  authors:
12
12
  - Pjotr Prins
@@ -14,7 +14,7 @@ autorequire:
14
14
  bindir: bin
15
15
  cert_chain: []
16
16
 
17
- date: 2011-01-13 00:00:00 +01:00
17
+ date: 2011-01-17 00:00:00 +01:00
18
18
  default_executable: gff3-fetch
19
19
  dependencies:
20
20
  - !ruby/object:Gem::Dependency
@@ -33,50 +33,50 @@ dependencies:
33
33
  prerelease: false
34
34
  version_requirements: *id001
35
35
  - !ruby/object:Gem::Dependency
36
- name: bio-logger
36
+ name: log4r
37
37
  requirement: &id002 !ruby/object:Gem::Requirement
38
38
  none: false
39
39
  requirements:
40
40
  - - ">"
41
41
  - !ruby/object:Gem::Version
42
42
  segments:
43
- - 0
44
- - 5
45
- - 0
46
- version: 0.5.0
43
+ - 1
44
+ - 1
45
+ - 6
46
+ version: 1.1.6
47
47
  type: :runtime
48
48
  prerelease: false
49
49
  version_requirements: *id002
50
50
  - !ruby/object:Gem::Dependency
51
- name: shoulda
51
+ name: bio-logger
52
52
  requirement: &id003 !ruby/object:Gem::Requirement
53
53
  none: false
54
54
  requirements:
55
- - - ">="
55
+ - - ">"
56
56
  - !ruby/object:Gem::Version
57
57
  segments:
58
58
  - 0
59
- version: "0"
60
- type: :development
59
+ - 8
60
+ - 0
61
+ version: 0.8.0
62
+ type: :runtime
61
63
  prerelease: false
62
64
  version_requirements: *id003
63
65
  - !ruby/object:Gem::Dependency
64
- name: bundler
66
+ name: shoulda
65
67
  requirement: &id004 !ruby/object:Gem::Requirement
66
68
  none: false
67
69
  requirements:
68
- - - ~>
70
+ - - ">="
69
71
  - !ruby/object:Gem::Version
70
72
  segments:
71
- - 1
72
- - 0
73
73
  - 0
74
- version: 1.0.0
74
+ version: "0"
75
75
  type: :development
76
76
  prerelease: false
77
77
  version_requirements: *id004
78
78
  - !ruby/object:Gem::Dependency
79
- name: jeweler
79
+ name: bundler
80
80
  requirement: &id005 !ruby/object:Gem::Requirement
81
81
  none: false
82
82
  requirements:
@@ -84,99 +84,55 @@ dependencies:
84
84
  - !ruby/object:Gem::Version
85
85
  segments:
86
86
  - 1
87
- - 5
88
- - 2
89
- version: 1.5.2
87
+ - 0
88
+ - 0
89
+ version: 1.0.0
90
90
  type: :development
91
91
  prerelease: false
92
92
  version_requirements: *id005
93
93
  - !ruby/object:Gem::Dependency
94
- name: rcov
94
+ name: jeweler
95
95
  requirement: &id006 !ruby/object:Gem::Requirement
96
96
  none: false
97
97
  requirements:
98
- - - ">="
98
+ - - ~>
99
99
  - !ruby/object:Gem::Version
100
100
  segments:
101
- - 0
102
- version: "0"
101
+ - 1
102
+ - 5
103
+ - 2
104
+ version: 1.5.2
103
105
  type: :development
104
106
  prerelease: false
105
107
  version_requirements: *id006
106
108
  - !ruby/object:Gem::Dependency
107
- name: rspec
109
+ name: rcov
108
110
  requirement: &id007 !ruby/object:Gem::Requirement
109
111
  none: false
110
112
  requirements:
111
113
  - - ">="
112
114
  - !ruby/object:Gem::Version
113
115
  segments:
114
- - 2
115
- - 0
116
116
  - 0
117
- version: 2.0.0
117
+ version: "0"
118
118
  type: :development
119
119
  prerelease: false
120
120
  version_requirements: *id007
121
121
  - !ruby/object:Gem::Dependency
122
- name: bio
122
+ name: rspec
123
123
  requirement: &id008 !ruby/object:Gem::Requirement
124
124
  none: false
125
125
  requirements:
126
126
  - - ">="
127
- - !ruby/object:Gem::Version
128
- segments:
129
- - 1
130
- - 4
131
- - 1
132
- version: 1.4.1
133
- type: :runtime
134
- prerelease: false
135
- version_requirements: *id008
136
- - !ruby/object:Gem::Dependency
137
- name: log4r
138
- requirement: &id009 !ruby/object:Gem::Requirement
139
- none: false
140
- requirements:
141
- - - ">"
142
- - !ruby/object:Gem::Version
143
- segments:
144
- - 1
145
- - 1
146
- - 6
147
- version: 1.1.6
148
- type: :runtime
149
- prerelease: false
150
- version_requirements: *id009
151
- - !ruby/object:Gem::Dependency
152
- name: bio-logger
153
- requirement: &id010 !ruby/object:Gem::Requirement
154
- none: false
155
- requirements:
156
- - - ">="
157
- - !ruby/object:Gem::Version
158
- segments:
159
- - 0
160
- - 6
161
- - 1
162
- version: 0.6.1
163
- type: :runtime
164
- prerelease: false
165
- version_requirements: *id010
166
- - !ruby/object:Gem::Dependency
167
- name: rspec
168
- requirement: &id011 !ruby/object:Gem::Requirement
169
- none: false
170
- requirements:
171
- - - ">"
172
127
  - !ruby/object:Gem::Version
173
128
  segments:
174
129
  - 2
130
+ - 3
175
131
  - 0
176
- version: "2.0"
132
+ version: 2.3.0
177
133
  type: :development
178
134
  prerelease: false
179
- version_requirements: *id011
135
+ version_requirements: *id008
180
136
  description: |
181
137
  GFF3 (genome browser) information and digest mRNA and CDS sequences.
182
138
  Options for low memory use and caching of records.
@@ -200,7 +156,9 @@ files:
200
156
  - bin/gff3-fetch
201
157
  - bio-gff3.gemspec
202
158
  - lib/bio-gff3.rb
159
+ - lib/bio/db/gff/block/gffblockparser.rb
203
160
  - lib/bio/db/gff/digest/gffinmemory.rb
161
+ - lib/bio/db/gff/digest/gfflrucache.rb
204
162
  - lib/bio/db/gff/digest/gffnocache.rb
205
163
  - lib/bio/db/gff/digest/gffparser.rb
206
164
  - lib/bio/db/gff/file/gfffasta.rb
@@ -234,6 +192,8 @@ files:
234
192
  - test/data/gff/test.gff3
235
193
  - test/data/regression/test_ext_gff3.rtest
236
194
  - test/data/regression/test_gff3.rtest
195
+ - test/data/regression/test_lrucache_ext_gff3.rtest
196
+ - test/data/regression/test_lrucache_gff3.rtest
237
197
  - test/data/regression/test_nocache_ext_gff3.rtest
238
198
  - test/data/regression/test_nocache_gff3.rtest
239
199
  - test/helper.rb