bio-gff3 0.6.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (35) hide show
  1. data/Gemfile +14 -0
  2. data/Gemfile.lock +22 -0
  3. data/LICENSE.txt +20 -0
  4. data/README +65 -0
  5. data/README.rdoc +19 -0
  6. data/Rakefile +56 -0
  7. data/VERSION +1 -0
  8. data/bin/gff3-fetch +99 -0
  9. data/bio-gff3.gemspec +101 -0
  10. data/lib/bio-gff3.rb +0 -0
  11. data/lib/bio/db/gff/gffassemble.rb +300 -0
  12. data/lib/bio/db/gff/gffdb.rb +40 -0
  13. data/lib/bio/db/gff/gfffasta.rb +68 -0
  14. data/lib/bio/db/gff/gfffileiterator.rb +77 -0
  15. data/lib/bio/db/gff/gffinmemory.rb +63 -0
  16. data/lib/bio/db/gff/gffnocache.rb +124 -0
  17. data/lib/bio/db/gff/gffparser.rb +154 -0
  18. data/lib/bio/system/lruhash.rb +268 -0
  19. data/spec/gff3_assemble2_spec.rb +73 -0
  20. data/spec/gff3_assemble3_spec.rb +62 -0
  21. data/spec/gff3_assemble_spec.rb +291 -0
  22. data/spec/gff3_fileiterator_spec.rb +43 -0
  23. data/spec/gffdb_spec.rb +99 -0
  24. data/test/data/gff/MhA1_Contig1133.fa +2 -0
  25. data/test/data/gff/MhA1_Contig1133.gff3 +1862 -0
  26. data/test/data/gff/MhA1_Contig125.fa +673 -0
  27. data/test/data/gff/MhA1_Contig125.gff3 +2177 -0
  28. data/test/data/gff/standard.gff3 +25 -0
  29. data/test/data/gff/test-cds.gff3 +98 -0
  30. data/test/data/gff/test-ext-fasta.fa +16 -0
  31. data/test/data/gff/test-ext-fasta.gff3 +57 -0
  32. data/test/data/gff/test.gff3 +74 -0
  33. data/test/helper.rb +18 -0
  34. data/test/test_bio-gff3.rb +7 -0
  35. metadata +180 -0
data/test/data/gff/standard.gff3 ADDED
@@ -0,0 +1,25 @@
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+ ##gff-version 3 ##sequence-region
2
+ ctg123 1 1497228
3
+ ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
4
+ ctg123 . TF_binding_site 1000 1012 . + . Parent=gene00001
5
+ ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001
6
+ ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001
7
+ ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001
8
+ ctg123 . exon 1300 1500 . + . Parent=mRNA00003
9
+ ctg123 . exon 1050 1500 . + . Parent=mRNA00001,mRNA00002
10
+ ctg123 . exon 3000 3902 . + . Parent=mRNA00001,mRNA00003
11
+ ctg123 . exon 5000 5500 . + . Parent=mRNA00001,mRNA00002,mRNA00003
12
+ ctg123 . exon 7000 9000 . + . Parent=mRNA00001,mRNA00002,mRNA00003
13
+ ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001
14
+ ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001
15
+ ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001
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+ ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001
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+ ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002
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+ ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002
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+ ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002
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+ ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003
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+ ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003
22
+ ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003
23
+ ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003
24
+ ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003
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+ ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003
data/test/data/gff/test-cds.gff3 ADDED
@@ -0,0 +1,98 @@
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+ ##gff-version 3 ##sequence-regio
2
+ # Gene gene:MhA1_Contig1040.frz3.gene29
3
+ MhA1_Contig1040 WormBase gene 1 182 . - . ID=gene:MhA1_Contig1040.frz3.gene29;Name=MhA1_Contig1040.frz3.gene29;Note=PREDICTED protein_coding;public_name=MhA1_Contig1040.frz3.gene29
4
+ MhA1_Contig1040 WormBase mRNA 1 182 . - . ID=transcript:MhA1_Contig1040.
5
+ frz3.gene29;Parent=gene:MhA1_Contig1040.frz3.gene29;Name=MhA1_Contig1040.frz3.ge
6
+ ne29;public_name=MhA1_Contig1040.frz3.gene29
7
+ MhA1_Contig1040 WormBase exon 1 182 . - . ID=exon:MhA1_Contig1040.frz3.g
8
+ ene29.1;Parent=transcript:MhA1_Contig1040.frz3.gene29
9
+ MhA1_Contig1040 WormBase CDS 1 180 . - 2 ID=cds:MhA1_Contig1040.frz3.gene
10
+ 29;Parent=transcript:MhA1_Contig1040.frz3.gene29
11
+
12
+ ##gff-version 3 ##sequence-regio
13
+ # Gene gene:MhA1_Contig2992.frz3.gene1
14
+ 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
15
+ MhA1_Contig2992 WormBase mRNA 577 2176 . - . ID=transcript:MhA1_Contig2992.frz3.gene1;Parent=gene:MhA1_Contig2992.frz3.gene1;Name=MhA1_Contig2992.frz3.gene1;public_name=MhA1_Contig2992.frz3.gene1
16
+ MhA1_Contig2992 WormBase exon 2078 2176 . - . ID=exon:MhA1_Contig2992.frz3.gene1.1;Parent=transcript:MhA1_Contig2992.frz3.gene1
17
+ MhA1_Contig2992 WormBase exon 1692 1944 . - . ID=exon:MhA1_Contig2992.frz3.gene1.2;Parent=transcript:MhA1_Contig2992.frz3.gene1
18
+ MhA1_Contig2992 WormBase exon 1439 1587 . - . ID=exon:MhA1_Contig2992.frz3.gene1.3;Parent=transcript:MhA1_Contig2992.frz3.gene1
19
+ MhA1_Contig2992 WormBase exon 1096 1241 . - . ID=exon:MhA1_Contig2992.frz3.gene1.4;Parent=transcript:MhA1_Contig2992.frz3.gene1
20
+ MhA1_Contig2992 WormBase exon 927 1049 . - . ID=exon:MhA1_Contig2992.frz3.gene1.5;Parent=transcript:MhA1_Contig2992.frz3.gene1
21
+ MhA1_Contig2992 WormBase exon 577 732 . - . ID=exon:MhA1_Contig2992.frz3.gene1.6;Parent=transcript:MhA1_Contig2992.frz3.gene1
22
+ MhA1_Contig2992 WormBase CDS 2078 2174 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
23
+ MhA1_Contig2992 WormBase CDS 1692 1944 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
24
+ MhA1_Contig2992 WormBase CDS 1439 1587 . - 1 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
25
+ MhA1_Contig2992 WormBase CDS 1096 1241 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
26
+ MhA1_Contig2992 WormBase CDS 927 1049 . - 0 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
27
+ MhA1_Contig2992 WormBase CDS 577 732 . - 0 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
28
+ MhA1_Contig2992 blat_nembase_ests nucleotide_match 1778 2214 45.29 - . ID=blat_nembase_ests.1828564;Name=MJC03471;Target=MJC03471 88 372;Gap=30M29D31I66M165D11I27M18I33M19D22I10M21D37M
29
+ MhA1_Contig2992 blat_washu_ests nucleotide_match 1529 2164 36.82 - . ID=blat_washu_ests.2375120;Name=MJ04126;Target=MJ04126 159 530;Gap=80M159D5I24M56D77I12M21D38M3I48M131D18I67M
30
+ MhA1_Contig2992 blat_washu_ests nucleotide_match 1778 2214 34.08 - . ID=blat_washu_ests.2425103;Name=MJ04126;Target=MJ04126 106 391;Gap=59M3I66M165D11I27M18I33M19D22I10M21D37M
31
+ MhA1_Contig2992 TRF repeat_region 83 147 102 - . ID=TRF.57974
32
+ MhA1_Contig2992 RepeatMask repeat_region 169 404 2011 - . ID=RepeatMask.324631
33
+ MhA1_Contig2992 Dust repeat_region 397 405 . - . ID=Dust.42101
34
+ MhA1_Contig2992 RepeatMask repeat_region 405 565 35 + . ID=RepeatMask.324632
35
+ MhA1_Contig2992 Dust repeat_region 493 565 . - . ID=Dust.42102
36
+ MhA1_Contig2992 RepeatMask repeat_region 1243 1266 24 + . ID=RepeatMask.324633
37
+ MhA1_Contig2992 RepeatMask repeat_region 1695 1834 200 + . ID=RepeatMask.324634
38
+ MhA1_Contig2992 Dust repeat_region 1709 1795 . - . ID=Dust.42103
39
+ MhA1_Contig2992 Dust repeat_region 1881 1931 . - . ID=Dust.42104
40
+ MhA1_Contig2992 Dust repeat_region 1944 2071 . - . ID=Dust.42105
41
+ MhA1_Contig2992 RepeatMask repeat_region 1946 2076 45 + . ID=RepeatMask.324635
42
+ MhA1_Contig2992 RepeatMask repeat_region 2136 2257 66 + . ID=RepeatMask.324636
43
+ MhA1_Contig2992 Dust repeat_region 2159 2281 . - . ID=Dust.42107
44
+ MhA1_Contig2992 TRF repeat_region 2305 2364 76 - . ID=TRF.57978
45
+ MhA1_Contig2992 Dust repeat_region 2319 2380 . - . ID=Dust.42109
46
+ MhA1_Contig2992 RepeatMask repeat_region 2333 2437 42 + . ID=RepeatMask.324637
47
+ MhA1_Contig2992 Dust repeat_region 2395 2437 . - . ID=Dust.42110
48
+ MhA1_Contig2992 TRF repeat_region 2688 2730 56 - . ID=TRF.57984
49
+ MhA1_Contig2992 RepeatMask repeat_region 2957 3019 28 + . ID=RepeatMask.324638
50
+ MhA1_Contig2992 Dust repeat_region 2959 3019 . - . ID=Dust.42112
51
+ MhA1_Contig2992 RepeatMask repeat_region 3194 3237 23 + . ID=RepeatMask.324639
52
+ MhA1_Contig2992 Dust repeat_region 3222 3277 . - . ID=Dust.42114
53
+ ##FASTA
54
+ >MhA1_Contig2992
55
+ TTTTGGTGACCAAAGTTCCTATTGGTGACCAAAATTCCAGTGCCCAATATTCCGTTTTTTGACTTGGTGACCAAAATTCC
56
+ GCTGGTGACCAAAATTCCAAAAAATTGGTGACCAAAGTTCCGAAAAATCTTGGTGACCAAAATTCCGGTGACCAAAATTC
57
+ TGGGACTCCTCAGGTTCGATGCCTGGCGGCAGCTGGTGGCCGGTTTAGTGTAGTCCCTGTATAGCACTTACACAGGTGGC
58
+ ACGCCCTGAGTGGGGAGGCAATTGGGTCTAGCGTGCTTGTAAATACCGAGCCGGCAAAAGGTATTGACACATCCACTAAC
59
+ AAGTATATGTAAATCCTTAACACTCCCCCTCCACATGTAAGTGCCTAAAAGCCTCTGTGGTTGATTTAATTACACCAAAA
60
+ AAAAATTATAAATTTTATTTTCTTAAACTTTTGTTTTATGATTTAATTAATTTATAACACATCATATTATTTAACCAGTT
61
+ TTCATAATTAGTAAATAATTTTTCATTCAATAAATTTCATGTAATTTAGAAATAAGAAAAATTTTAAAAAATTATAATTT
62
+ AAAAACGATTATTATTCTATGTAAGATTTGGCGGTATATTTCCATCTAATGGTCCAATAACAGATATTTGTCTTTGTAAT
63
+ TCCTGACGAATACTATCGTCTGTACCGCCGAGGATTTGTTCAATTTGAAGAATTAAAGCTCTTTCAGCAATATCAGGATT
64
+ ATTCAGAAGATCCTTTAAACTTTGAATTATTTGTAAATAAATGTAGGGATACTAAATTATTTTTATTAAATAGAGTTATT
65
+ TTACAGAAAAATATTCTATGAGGCAAAATAAAAGCAATATTTATTATTAAACTATCAAGCAATAAATTCTTTCCTTGACG
66
+ AAAATTTTTGACTTAAAAAAATCAGGCCTTAACAATTAATTATTACCTGAATTCTTTTATCAACATTCTGTGCATTTCTG
67
+ CTTAATTTAATTTGAACATTTCGTTGACGTTCACTTTTAAATTGTTTTTCTTTTTGTTGTAAAGATTGTTGAAATTGTTT
68
+ ATAAAGATCCTCAAAATAGAACAAATTTAATTGTTAACTCTAAAAATAAACAAACAGAAATTCTCTGCCCTTGTTGATCA
69
+ GCCCAATTCTGTTTATCTCTTCGTATAGAAGACTTGGACCTGTCATTTTCTGCTTCAAGTTGAAGAAATTTCTGACGCTC
70
+ TGAGAGACTGGCCGTTTTCAAAAATTCTGGTAATTGATCATCTAAATAAAATTTAAATATTAATTTGTTTCAACATTTAT
71
+ CCTTATATTTCTCAAATTTTCATTTAAATAACTTTCTTAATTCCAGATAACCCCAAATTTGTAATGTCTTTGTCATTCGA
72
+ CATAGAAAAACGAATCCATAAATTGGGCGAAGGATCCTTAAAATTTTCACGCCACGAAAATAAAAATATAAAGATTACCA
73
+ TTCGATCTTTTTAAATTATTTGTTCCATCTAATGTGCCGCTATCTAAGCCTCTTTGTGATTTATCATTATTGCCAGAATC
74
+ AAAACTATCACGTTGATTATTTCTGTCTTGATTCTGCTCATCAAACCTTTCAGAAGCCTTATTTCTTCTAAATTGTTAAA
75
+ TATTGAAATACTTTTTCGATCTCTAAGTATTATCGAAAATTAAAATATACAGTGATTTATTATAATAAAAGAACATAATT
76
+ TGATAACATACTCATTTTTATCCCTTCCTTTATTCCTTCCTAATTCATACTTTTCTATCATTCCTTTTTTCCCTTTCTTT
77
+ TTTCTATTATCCTCTTCTTTTTCATATTCACTTTCATTATCCCCAAAATTACTTATTTGTTTTTTGCTTTCTTTTGAAGG
78
+ TATTTCATTATTATCAAAACCTTCACTTTGAATATCCAACTCTTTATTTCCTTCTTTTTGATTTTTACCGAATTTTTTGT
79
+ TGCCTTTTTTTGTTGCTATATTGTCTAAATAAAATAATGTTAAAATCTAATTTAAATGTTAAAATTTAATTTGTGATTTT
80
+ TTTCAATTTTCGGCTTATAAAAATCTTTTTTTAAAAAACAAAATTTTAATTAAATAAGTTTTAATAAAAATATTTACCTT
81
+ CATTTTGTTCAGAATTAATTCCATCATTAAACAAATTTTCATTCGAATCAGATTGAATATTAAAAGAATTATCATTTATT
82
+ TTTTTATTAATTTTAGCTTTGATAATTAATAAATAAAAAGTAAATAATAATAATTTTATTAATATTTTCATATTAATTTT
83
+ AGAATTTTATTTATTTTGACAGTTAATAAGTATTATTATTAGAAAACTTGCCAATAATTGATTTCTAAATTTAAATGGAT
84
+ TTTTGTTTCAGCTAAATTTAAATGTTTTATTTCATTTAAATTTAGAAATTTATTATGTTTGTATAGCATTATTCAATAAT
85
+ TTTTAATAAATAAATTTAAATTTTTTGAATAAAAAATCGAGAAAACCTAAATTATATATTAAGAATTTCTAAATTTCTCG
86
+ AAGATATTTACAAAACAACTTGCAAAGTGATATTTTTTCTAAACATGTCAAAAGCCCTAATTATTACATGCATTAAAGCA
87
+ AAAATTTTCTTTTTAATATTTGAAATAAATTCCAATCAAAGGATTTACGATAATCAAGAAATAATATAGTTCATATATTC
88
+ TAATAAAGTCTTTAATATAATATACCTAGTCTTTAGAAGTAGAATTCAGAAAAGTTTATAAAGAAGAGAAATAGTTTAAA
89
+ GGAAAGAAAAAATCATTCAAAAATTGTTTTCTTATCATATATTCTTTACATCTTTTGAAGTTTGTGTATAAACCAAATTG
90
+ TAGAATATATTGAAAATAAAATCACTCCAATAATAATTAACAAAATACATAAAAAATGGCGTGGTTGACAACCGCATTTT
91
+ CTCTCAATATCGAAGCCACGTTTGCGGCGATTTTTATTTTGAAGAGGAAAATCTGATATTTATTGTATAGATTTAGTTAT
92
+ TTAATAATTAAATTTCAAAAATTACTTGTCTTATTTAATCTTTTATTTATTTTATTTTTGCATTCAAAAGAAGGAATCTC
93
+ AAATTTTAAAGTAAATGCTTTCCAAATTGAAATAGCCATATCAAAAGATCCTTCATTTATTAAAGGTTCTTTTCTCACAA
94
+ TAATATTCTCCATTTCTTTCCAATCAAAATTATTCTTTATTTCAAAACTATTCCAAAAATTATCCAAAATTCCAATTAAA
95
+ TATTTTTTGTTAAATAAAAGGTTTAAATTAATTATTTGTGCTTTTTCGAATTTTTCATTTAAATCCTTTATTTTTTTGAA
96
+ ATTATCATAAAGCTCTAATGATGCTTTTTGAATTTTTGAGACATTTTCAATATCAAAATTTGGTCCGGAAAATTTATTTA
97
+ >MhA1_Contig1040
98
+ TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAAAC
data/test/data/gff/test-ext-fasta.fa ADDED
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+ >test01
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+ ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
3
+ GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
4
+ CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
5
+ AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
6
+ GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
7
+ CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
8
+ >test02
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+ ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
10
+ GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
11
+ CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
12
+ AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
13
+ GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
14
+ CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
15
+
16
+
data/test/data/gff/test-ext-fasta.gff3 ADDED
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+ ##gff-version 3
2
+ ## sequence-region Contig1 1 37450
3
+ Contig1 confirmed transcript 1001 2000 42 + . ID=Transcript:trans-1;Gene=abc-1;Gene=xyz-2;Note=function+unknown
4
+ Contig1 confirmed exon 1001 1100 . + . ID=Transcript:trans-1
5
+ Contig1 confirmed exon 1201 1300 . + . ID=Transcript:trans-1
6
+ Contig1 confirmed exon 1401 1450 . + . ID=Transcript:trans-1
7
+ Contig1 confirmed CDS 1051 1100 . + 0 ID=Transcript:trans-1
8
+ Contig1 confirmed CDS 1201 1300 . + 2 ID=Transcript:trans-1
9
+ Contig1 confirmed CDS 1401 1440 . + 0 ID=Transcript:trans-1
10
+ Contig1 est similarity 1001 1100 96 . . Target=EST:CEESC13F 1 100 +
11
+ Contig1 est similarity 1201 1300 99 . . Target=EST:CEESC13F 101 200 +
12
+ Contig1 est similarity 1401 1450 99 . . Target=EST:CEESC13F 201 250 +
13
+ Contig1 tc1 transposon 5001 6000 . + . ID=Transposon:c128.1
14
+ Contig1 tc1 transposon 8001 9000 . - . ID=Transposon:c128.2
15
+ Contig1 confirmed transcript 30001 31000 . - . ID=Transcript:trans-2;Gene=xyz-2;Note=Terribly+interesting
16
+ Contig1 confirmed exon 30001 30100 . - . ID=Transcript:trans-2;Gene=abc-1;Note=function+unknown
17
+ Contig1 confirmed exon 30701 30800 . - . ID=Transcript:trans-2
18
+ Contig1 confirmed exon 30801 31000 . - . ID=Transcript:trans-2
19
+
20
+ ## sequence-region Contig2 1 37450
21
+ Contig2 clone Component 1 2000 . . . Target=Clone:AL12345.1 1 2000 +;Note=Terribly+interesting
22
+ Contig2 clone Component 2001 5000 . . . Target=Clone:AL11111.1 6000 3001 +
23
+ Contig2 clone Component 5001 20000 . . . Target=Clone:AC13221.2 1 15000 +
24
+ Contig2 clone Component 2001 37450 . . . Target=Clone:M7.3 1001 36450 +
25
+ Contig2 predicted transcript 2501 4500 . + . ID=Transcript:trans-3;Alias=trans-18
26
+ Contig2 predicted transcript 5001 8001 . - . ID=Transcript:trans-4
27
+
28
+
29
+ #processed_transcript
30
+ Contig3 clone Component 1 50000 . . . ID=Clone:AL12345.2
31
+ Contig3 confirmed mRNA 32000 35000 . + . ID=mRNA:trans-8
32
+ Contig3 confirmed UTR 32000 32100 . + . ID=mRNA:trans-8
33
+ Contig3 confirmed CDS 32101 33000 . + . ID=mRNA:trans-8
34
+ Contig3 confirmed CDS 34000 34500 . + . ID=mRNA:trans-8
35
+ Contig3 confirmed CDS 34600 34900 . + . ID=mRNA:trans-8
36
+ Contig3 confirmed UTR 34901 35000 . + . ID=mRNA:trans-8
37
+
38
+ ## preferred group assignments
39
+ Contig4 clone Component 1 50000 . . . ID=Clone:ABC123
40
+ Contig4 confirmed gene 32000 35000 . + . ID=Misc:thing1;gene=gene-9
41
+ Contig4 confirmed mRNA 32000 35000 . + . ID=Misc:thing2;mRNA=trans-9;gene=gene-9
42
+ Contig4 confirmed CDS 32000 35000 . + . ID=Misc:thing3;mRNA=trans-9
43
+
44
+ ##gff-version 3
45
+ ##sequence-region test01 1 400
46
+ test01 RANDOM contig 1 400 . + . ID=test01;Note=this is test
47
+ test01 . mRNA 3 14 . + . ID=mrna01short;Name=testmRNA;Note=this is test mRNA
48
+ test01 . mRNA 101 230 . + . ID=mrna01;Name=testmRNA;Note=this is test mRNA
49
+ test01 . mRNA 101 280 . + . ID=mrna01a;Name=testmRNAalterative;Note=test of alternative splicing variant
50
+ test01 . exon 101 160 . + . ID=exon01;Name=exon01;Alias=exon 1;Parent=mrna01,mrna01a
51
+ test01 . exon 201 230 . + . ID=exon02;Name=exon02;Alias=exon 2;Parent=mrna01
52
+ test01 . exon 251 280 . + . ID=exon02a;Name=exon02a;Alias=exon 2a;Parent=mrna01a
53
+ test01 . CDS 3 14 . + . ID=cds_short;Name=testmRNA;Parent=mrna01short;Note=this is test mRNA
54
+ test01 . CDS 192 200 . + . ID=cds1;Parent=mrna01a
55
+ test01 . CDS 164 190 . + . ID=cds1;Parent=mrna01a
56
+ test01 . CDS 192 200 . + . ID=cds2;Parent=mrna01a
57
+ test01 . Match 101 123 . . . ID=match01;Name=match01;Target=EST101 1 21;Gap=M8 D3 M6 I1 M6
data/test/data/gff/test.gff3 ADDED
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1
+ ##gff-version 3
2
+ ## sequence-region Contig1 1 37450
3
+ Contig1 confirmed transcript 1001 2000 42 + . ID=Transcript:trans-1;Gene=abc-1;Gene=xyz-2;Note=function+unknown
4
+ Contig1 confirmed exon 1001 1100 . + . ID=Transcript:trans-1
5
+ Contig1 confirmed exon 1201 1300 . + . ID=Transcript:trans-1
6
+ Contig1 confirmed exon 1401 1450 . + . ID=Transcript:trans-1
7
+ Contig1 confirmed CDS 1051 1100 . + 0 ID=Transcript:trans-1
8
+ Contig1 confirmed CDS 1201 1300 . + 2 ID=Transcript:trans-1
9
+ Contig1 confirmed CDS 1401 1440 . + 0 ID=Transcript:trans-1
10
+ Contig1 est similarity 1001 1100 96 . . Target=EST:CEESC13F 1 100 +
11
+ Contig1 est similarity 1201 1300 99 . . Target=EST:CEESC13F 101 200 +
12
+ Contig1 est similarity 1401 1450 99 . . Target=EST:CEESC13F 201 250 +
13
+ Contig1 tc1 transposon 5001 6000 . + . ID=Transposon:c128.1
14
+ Contig1 tc1 transposon 8001 9000 . - . ID=Transposon:c128.2
15
+ Contig1 confirmed transcript 30001 31000 . - . ID=Transcript:trans-2;Gene=xyz-2;Note=Terribly+interesting
16
+ Contig1 confirmed exon 30001 30100 . - . ID=Transcript:trans-2;Gene=abc-1;Note=function+unknown
17
+ Contig1 confirmed exon 30701 30800 . - . ID=Transcript:trans-2
18
+ Contig1 confirmed exon 30801 31000 . - . ID=Transcript:trans-2
19
+
20
+ ## sequence-region Contig2 1 37450
21
+ Contig2 clone Component 1 2000 . . . Target=Clone:AL12345.1 1 2000 +;Note=Terribly+interesting
22
+ Contig2 clone Component 2001 5000 . . . Target=Clone:AL11111.1 6000 3001 +
23
+ Contig2 clone Component 5001 20000 . . . Target=Clone:AC13221.2 1 15000 +
24
+ Contig2 clone Component 2001 37450 . . . Target=Clone:M7.3 1001 36450 +
25
+ Contig2 predicted transcript 2501 4500 . + . ID=Transcript:trans-3;Alias=trans-18
26
+ Contig2 predicted transcript 5001 8001 . - . ID=Transcript:trans-4
27
+
28
+
29
+ #processed_transcript
30
+ Contig3 clone Component 1 50000 . . . ID=Clone:AL12345.2
31
+ Contig3 confirmed mRNA 32000 35000 . + . ID=mRNA:trans-8
32
+ Contig3 confirmed UTR 32000 32100 . + . ID=mRNA:trans-8
33
+ Contig3 confirmed CDS 32101 33000 . + . ID=mRNA:trans-8
34
+ Contig3 confirmed CDS 34000 34500 . + . ID=mRNA:trans-8
35
+ Contig3 confirmed CDS 34600 34900 . + . ID=mRNA:trans-8
36
+ Contig3 confirmed UTR 34901 35000 . + . ID=mRNA:trans-8
37
+
38
+ ## preferred group assignments
39
+ Contig4 clone Component 1 50000 . . . ID=Clone:ABC123
40
+ Contig4 confirmed gene 32000 35000 . + . ID=Misc:thing1;gene=gene-9
41
+ Contig4 confirmed mRNA 32000 35000 . + . ID=Misc:thing2;mRNA=trans-9;gene=gene-9
42
+ Contig4 confirmed CDS 32000 35000 . + . ID=Misc:thing3;mRNA=trans-9
43
+
44
+ ##gff-version 3
45
+ ##sequence-region test01 1 400
46
+ test01 RANDOM contig 1 400 . + . ID=test01;Note=this is test
47
+ test01 . mRNA 3 14 . + . ID=mrna01short;Name=testmRNA;Note=this is test mRNA
48
+ test01 . mRNA 101 230 . + . ID=mrna01;Name=testmRNA;Note=this is test mRNA
49
+ test01 . mRNA 101 280 . + . ID=mrna01a;Name=testmRNAalterative;Note=test of alternative splicing variant
50
+ test01 . exon 101 160 . + . ID=exon01;Name=exon01;Alias=exon 1;Parent=mrna01,mrna01a
51
+ test01 . exon 201 230 . + . ID=exon02;Name=exon02;Alias=exon 2;Parent=mrna01
52
+ test01 . exon 251 280 . + . ID=exon02a;Name=exon02a;Alias=exon 2a;Parent=mrna01a
53
+ test01 . CDS 3 14 . + . ID=cds_short;Name=testmRNA;Parent=mrna01short;Note=this is test mRNA
54
+ test01 . CDS 192 200 . + . ID=cds1;Parent=mrna01a
55
+ test01 . CDS 164 190 . + . ID=cds1;Parent=mrna01a
56
+ test01 . CDS 192 200 . + . ID=cds2;Parent=mrna01a
57
+ test01 . Match 101 123 . . . ID=match01;Name=match01;Target=EST101 1 21;Gap=M8 D3 M6 I1 M6
58
+ ##FASTA
59
+ >test01
60
+ ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
61
+ GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
62
+ CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
63
+ AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
64
+ GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
65
+ CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
66
+ >test02
67
+ ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
68
+ GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
69
+ CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
70
+ AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
71
+ GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
72
+ CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
73
+
74
+
data/test/helper.rb ADDED
@@ -0,0 +1,18 @@
1
+ require 'rubygems'
2
+ require 'bundler'
3
+ begin
4
+ Bundler.setup(:default, :development)
5
+ rescue Bundler::BundlerError => e
6
+ $stderr.puts e.message
7
+ $stderr.puts "Run `bundle install` to install missing gems"
8
+ exit e.status_code
9
+ end
10
+ require 'test/unit'
11
+ require 'shoulda'
12
+
13
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
14
+ $LOAD_PATH.unshift(File.dirname(__FILE__))
15
+ require 'bio-gff3'
16
+
17
+ class Test::Unit::TestCase
18
+ end
data/test/test_bio-gff3.rb ADDED
@@ -0,0 +1,7 @@
1
+ require 'helper'
2
+
3
+ class TestBioGff3 < Test::Unit::TestCase
4
+ should "probably rename this file and start testing for real" do
5
+ flunk "hey buddy, you should probably rename this file and start testing for real"
6
+ end
7
+ end
metadata ADDED
@@ -0,0 +1,180 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-gff3
3
+ version: !ruby/object:Gem::Version
4
+ prerelease: false
5
+ segments:
6
+ - 0
7
+ - 6
8
+ - 0
9
+ version: 0.6.0
10
+ platform: ruby
11
+ authors:
12
+ - Pjotr Prins
13
+ autorequire:
14
+ bindir: bin
15
+ cert_chain: []
16
+
17
+ date: 2010-12-29 00:00:00 +01:00
18
+ default_executable: gff3-fetch
19
+ dependencies:
20
+ - !ruby/object:Gem::Dependency
21
+ name: shoulda
22
+ requirement: &id001 !ruby/object:Gem::Requirement
23
+ none: false
24
+ requirements:
25
+ - - ">="
26
+ - !ruby/object:Gem::Version
27
+ segments:
28
+ - 0
29
+ version: "0"
30
+ type: :development
31
+ prerelease: false
32
+ version_requirements: *id001
33
+ - !ruby/object:Gem::Dependency
34
+ name: bundler
35
+ requirement: &id002 !ruby/object:Gem::Requirement
36
+ none: false
37
+ requirements:
38
+ - - ~>
39
+ - !ruby/object:Gem::Version
40
+ segments:
41
+ - 1
42
+ - 0
43
+ - 0
44
+ version: 1.0.0
45
+ type: :development
46
+ prerelease: false
47
+ version_requirements: *id002
48
+ - !ruby/object:Gem::Dependency
49
+ name: jeweler
50
+ requirement: &id003 !ruby/object:Gem::Requirement
51
+ none: false
52
+ requirements:
53
+ - - ~>
54
+ - !ruby/object:Gem::Version
55
+ segments:
56
+ - 1
57
+ - 5
58
+ - 2
59
+ version: 1.5.2
60
+ type: :development
61
+ prerelease: false
62
+ version_requirements: *id003
63
+ - !ruby/object:Gem::Dependency
64
+ name: rcov
65
+ requirement: &id004 !ruby/object:Gem::Requirement
66
+ none: false
67
+ requirements:
68
+ - - ">="
69
+ - !ruby/object:Gem::Version
70
+ segments:
71
+ - 0
72
+ version: "0"
73
+ type: :development
74
+ prerelease: false
75
+ version_requirements: *id004
76
+ - !ruby/object:Gem::Dependency
77
+ name: bio
78
+ requirement: &id005 !ruby/object:Gem::Requirement
79
+ none: false
80
+ requirements:
81
+ - - ">="
82
+ - !ruby/object:Gem::Version
83
+ segments:
84
+ - 1
85
+ - 4
86
+ - 1
87
+ version: 1.4.1
88
+ type: :development
89
+ prerelease: false
90
+ version_requirements: *id005
91
+ description: |
92
+ GFF3 (genome browser) information and digest mRNA and CDS sequences.
93
+ Options for low memory use and caching of records.
94
+ Support for external FASTA files.
95
+
96
+ email: pjotr.prins@thebird.nl
97
+ executables:
98
+ - gff3-fetch
99
+ extensions: []
100
+
101
+ extra_rdoc_files:
102
+ - LICENSE.txt
103
+ - README
104
+ - README.rdoc
105
+ files:
106
+ - Gemfile
107
+ - Gemfile.lock
108
+ - LICENSE.txt
109
+ - README
110
+ - README.rdoc
111
+ - Rakefile
112
+ - VERSION
113
+ - bin/gff3-fetch
114
+ - bio-gff3.gemspec
115
+ - lib/bio-gff3.rb
116
+ - lib/bio/db/gff/gffassemble.rb
117
+ - lib/bio/db/gff/gffdb.rb
118
+ - lib/bio/db/gff/gfffasta.rb
119
+ - lib/bio/db/gff/gfffileiterator.rb
120
+ - lib/bio/db/gff/gffinmemory.rb
121
+ - lib/bio/db/gff/gffnocache.rb
122
+ - lib/bio/db/gff/gffparser.rb
123
+ - lib/bio/system/lruhash.rb
124
+ - spec/gff3_assemble2_spec.rb
125
+ - spec/gff3_assemble3_spec.rb
126
+ - spec/gff3_assemble_spec.rb
127
+ - spec/gff3_fileiterator_spec.rb
128
+ - spec/gffdb_spec.rb
129
+ - test/data/gff/MhA1_Contig1133.fa
130
+ - test/data/gff/MhA1_Contig1133.gff3
131
+ - test/data/gff/MhA1_Contig125.fa
132
+ - test/data/gff/MhA1_Contig125.gff3
133
+ - test/data/gff/standard.gff3
134
+ - test/data/gff/test-cds.gff3
135
+ - test/data/gff/test-ext-fasta.fa
136
+ - test/data/gff/test-ext-fasta.gff3
137
+ - test/data/gff/test.gff3
138
+ - test/helper.rb
139
+ - test/test_bio-gff3.rb
140
+ has_rdoc: true
141
+ homepage: http://github.com/pjotrp/bioruby-gff3
142
+ licenses:
143
+ - MIT
144
+ post_install_message:
145
+ rdoc_options: []
146
+
147
+ require_paths:
148
+ - lib
149
+ required_ruby_version: !ruby/object:Gem::Requirement
150
+ none: false
151
+ requirements:
152
+ - - ">="
153
+ - !ruby/object:Gem::Version
154
+ hash: -266764915
155
+ segments:
156
+ - 0
157
+ version: "0"
158
+ required_rubygems_version: !ruby/object:Gem::Requirement
159
+ none: false
160
+ requirements:
161
+ - - ">="
162
+ - !ruby/object:Gem::Version
163
+ segments:
164
+ - 0
165
+ version: "0"
166
+ requirements: []
167
+
168
+ rubyforge_project:
169
+ rubygems_version: 1.3.7
170
+ signing_key:
171
+ specification_version: 3
172
+ summary: BioRuby GFF3 plugin for big data
173
+ test_files:
174
+ - spec/gff3_assemble2_spec.rb
175
+ - spec/gff3_assemble3_spec.rb
176
+ - spec/gff3_assemble_spec.rb
177
+ - spec/gff3_fileiterator_spec.rb
178
+ - spec/gffdb_spec.rb
179
+ - test/helper.rb
180
+ - test/test_bio-gff3.rb