bio-gff3 0.8.7 → 0.9.0
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- data/.travis.yml +12 -0
- data/Gemfile +4 -4
- data/Gemfile.lock +34 -20
- data/README.rdoc +22 -13
- data/Rakefile +24 -23
- data/VERSION +1 -1
- data/bin/gff3-fetch +15 -11
- data/bio-gff3.gemspec +30 -39
- data/lib/bio/db/gff/block/gffblockparser.rb +3 -4
- data/lib/bio/db/gff/digest/gfflrucache.rb +2 -1
- data/lib/bio/db/gff/digest/gffnocache.rb +2 -1
- data/lib/bio/db/gff/digest/gffparser.rb +5 -3
- data/lib/bio/db/gff/gffcomponent.rb +6 -5
- data/lib/bio/db/gff/gffsequence.rb +1 -1
- data/lib/bio/db/gff/gffvalidate.rb +2 -1
- data/spec/gff3_fileiterator_spec.rb +3 -4
- data/test/data/gff/m_hapla.WS232.annotations.part.gff3 +3725 -0
- data/test/data/gff/m_hapla.WS232.genomic.part.fa +3187 -0
- data/test/data/regression/test_ext_gff3.rtest +1 -5
- data/test/data/regression/test_gff3.rtest +1 -5
- data/test/data/regression/test_latest_wormbase_ext_gff3.ref +7885 -0
- data/test/data/regression/test_latest_wormbase_ext_gff3.rtest +280 -0
- data/test/data/regression/test_lrucache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_lrucache_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_gff3.rtest +1 -3
- data/test/helper.rb +1 -0
- data/test/{regressiontest.rb → regressiontest2.rb} +5 -5
- data/test/test_bio-gff3.rb +35 -10
- metadata +35 -36
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@@ -0,0 +1,280 @@
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INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
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2
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene1> <>
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3
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4027 4090> <>
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4
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4141 4251> <>
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5
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4311 4390> <>
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6
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4471 4576> <>
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7
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4635 4678> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4760 4959> <>
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9
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5070 5193> <>
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10
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5243 5274> <>
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11
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5348 5631> <>
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12
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5747 5841> <>
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13
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5881 5970> <>
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14
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene2> <>
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15
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INFO bio-gff3: Adding CDS <MhA1_Contig0 28712 28876> <>
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16
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INFO bio-gff3: Adding CDS <MhA1_Contig0 28918 29022> <>
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17
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29230 29583> <>
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18
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29626 29910> <>
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19
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29987 30067> <>
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20
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INFO bio-gff3: Adding CDS <MhA1_Contig0 30928 30968> <>
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21
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31014 31121> <>
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22
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31815 31900> <>
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23
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31943 32141> <>
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24
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32186 32403> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32453 32476> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32517 32705> <>
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27
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32741 32976> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33022 33211> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33255 33346> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33389 33535> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33578 33772> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33818 33936> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33989 34132> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34177 34273> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34353 34395> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34806 34966> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35014 35316> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35359 35649> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35697 35857> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35901 36060> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 36103 36216> <>
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42
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene3> <>
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43
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6259 6360> <>
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44
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6396 6564> <>
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45
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6611 6789> <>
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46
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6952 7028> <>
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47
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7090 7246> <>
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48
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7294 7407> <>
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49
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7465 7563> <>
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50
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene4> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48426 48702> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48745 48842> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48941 49079> <>
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54
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49154 49239> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49416 49514> <>
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56
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49687 49874> <>
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57
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49918 50002> <>
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58
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50379 50524> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50570 50663> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50706 50837> <>
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61
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50889 50945> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51018 51146> <>
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63
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51186 51388> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51434 51551> <>
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65
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene5> <>
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66
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INFO bio-gff3: Adding CDS <MhA1_Contig0 70770 71039> <>
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67
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71091 71262> <>
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68
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71334 71722> <>
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69
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71766 72038> <>
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70
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72093 72326> <>
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71
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72387 72500> <>
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72
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72542 72698> <>
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73
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72745 72938> <>
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74
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72984 73162> <>
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75
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73209 73455> <>
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76
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73599 73716> <>
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77
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73767 73855> <>
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78
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73900 74294> <>
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79
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74345 74438> <>
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80
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74484 74660> <>
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81
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74710 74729> <>
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82
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74773 74938> <>
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83
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75082 75207> <>
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84
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75259 75299> <>
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85
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75342 75405> <>
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86
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75461 75491> <>
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87
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75545 75639> <>
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88
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75690 75803> <>
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89
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75852 75926> <>
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90
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene6> <>
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91
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99137 99339> <>
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92
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99402 99529> <>
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93
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99573 99718> <>
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94
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100159 100348> <>
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95
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100488 100531> <>
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96
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100655 100714> <>
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97
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100770 100868> <>
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98
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100934 101021> <>
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99
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101065 101165> <>
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100
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101294 101419> <>
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101
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101587 101736> <>
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102
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101831 102034> <>
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103
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102076 102150> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102198 102414> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102503 102636> <>
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106
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene7> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 113735 113854> <>
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108
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INFO bio-gff3: Adding CDS <MhA1_Contig0 113898 113965> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114012 114105> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114148 114275> <>
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111
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114504 114633> <>
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112
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114678 114742> <>
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113
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114784 114861> <>
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114
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114907 115141> <>
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115
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115187 115252> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115302 115434> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115477 115596> <>
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118
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115640 115697> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115742 115803> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115843 115940> <>
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121
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115989 116150> <>
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122
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116198 116299> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116445 116616> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116662 116729> <>
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125
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene8> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44151 44252> <>
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127
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44288 44456> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44503 44681> <>
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129
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44728 44903> <>
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130
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45032 45128> <>
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131
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45175 45285> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45417 45569> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45887 46020> <>
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134
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47085 47165> <>
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135
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47370 47387> <>
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136
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47706 47769> <>
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137
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene9> <>
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138
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INFO bio-gff3: Adding CDS <MhA1_Contig0 180784 180984> <>
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139
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181219 181361> <>
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140
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181425 181624> <>
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141
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181793 181946> <>
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142
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INFO bio-gff3: Adding CDS <MhA1_Contig0 182296 182561> <>
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143
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INFO bio-gff3: Adding CDS <MhA1_Contig0 182881 183133> <>
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144
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INFO bio-gff3: Adding CDS <MhA1_Contig0 183291 183633> <>
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145
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INFO bio-gff3: Adding CDS <MhA1_Contig0 183889 184080> <>
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146
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184122 184262> <>
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147
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184446 184560> <>
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148
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184607 184737> <>
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149
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184784 184857> <>
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150
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185319 185622> <>
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151
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185693 185745> <>
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152
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185886 186126> <>
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153
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INFO bio-gff3: Adding CDS <MhA1_Contig0 186176 186300> <>
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154
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INFO bio-gff3: Adding CDS <MhA1_Contig0 186778 186843> <>
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155
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187036 187410> <>
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156
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187610 187785> <>
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157
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187984 188526> <>
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158
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188567 188673> <>
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159
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188733 188795> <>
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160
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188859 189164> <>
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161
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene10> <>
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162
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INFO bio-gff3: Adding CDS <MhA1_Contig0 223510 223611> <>
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163
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224103 224341> <>
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164
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224713 224870> <>
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165
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224917 225057> <>
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166
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INFO bio-gff3: Adding CDS <MhA1_Contig0 225522 225763> <>
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167
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226177 226291> <>
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168
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226342 226473> <>
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169
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226664 226758> <>
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170
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226961 227137> <>
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171
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227179 227259> <>
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172
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227558 227602> <>
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173
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227654 227836> <>
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174
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INFO bio-gff3: Adding CDS <MhA1_Contig0 228151 228220> <>
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175
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INFO bio-gff3: Adding CDS <MhA1_Contig0 228273 228596> <>
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176
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 228790 228932> <>
|
|
177
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229166 229309> <>
|
|
178
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229354 229407> <>
|
|
179
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229533 229760> <>
|
|
180
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229876 229998> <>
|
|
181
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230106 230153> <>
|
|
182
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230202 230314> <>
|
|
183
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230671 230825> <>
|
|
184
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231052 231134> <>
|
|
185
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231181 231246> <>
|
|
186
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231357 231470> <>
|
|
187
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231511 231677> <>
|
|
188
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231757 231826> <>
|
|
189
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231877 231975> <>
|
|
190
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 232359 232634> <>
|
|
191
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 232930 233188> <>
|
|
192
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 233542 233714> <>
|
|
193
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 233761 233929> <>
|
|
194
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 234240 234425> <>
|
|
195
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 234482 234675> <>
|
|
196
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235064 235171> <>
|
|
197
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235218 235311> <>
|
|
198
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235821 235995> <>
|
|
199
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 236262 236424> <>
|
|
200
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 236558 236572> <>
|
|
201
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig1.frz3.fgene1> <>
|
|
202
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 881 961> <>
|
|
203
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 1169 1355> <>
|
|
204
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 1417 1520> <>
|
|
205
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene11> <>
|
|
206
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 237099 237531> <>
|
|
207
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig4.frz3.fgene1> <>
|
|
208
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24120 24176> <>
|
|
209
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24219 24442> <>
|
|
210
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24710 24786> <>
|
|
211
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24833 24933> <>
|
|
212
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24980 25195> <>
|
|
213
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25300 25501> <>
|
|
214
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25714 25871> <>
|
|
215
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25916 26188> <>
|
|
216
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 26422 26523> <>
|
|
217
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig5.frz3.fgene1> <>
|
|
218
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 483 539> <>
|
|
219
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 583 806> <>
|
|
220
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1074 1150> <>
|
|
221
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1198 1298> <>
|
|
222
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1345 1616> <>
|
|
223
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1745 1866> <>
|
|
224
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 2079 2236> <>
|
|
225
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 2288 2554> <>
|
|
226
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig1.frz3.fgene2> <>
|
|
227
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 10506 10616> <>
|
|
228
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 10664 10726> <>
|
|
229
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11173 11278> <>
|
|
230
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11326 11440> <>
|
|
231
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11639 11918> <>
|
|
232
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig7.frz3.fgene1> <>
|
|
233
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73081 73141> <>
|
|
234
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73270 73419> <>
|
|
235
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73528 73656> <>
|
|
236
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 74057 74202> <>
|
|
237
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 74683 74723> <>
|
|
238
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75096 75202> <>
|
|
239
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75472 75548> <>
|
|
240
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75593 75694> <>
|
|
241
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig7.frz3.fgene2> <>
|
|
242
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 25361 25669> <>
|
|
243
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26231 26407> <>
|
|
244
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26786 26877> <>
|
|
245
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26920 27242> <>
|
|
246
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 27467 27749> <>
|
|
247
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 27802 27957> <>
|
|
248
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 28200 28272> <>
|
|
249
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig13.frz3.fgene1> <>
|
|
250
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 70665 70800> <>
|
|
251
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71061 71274> <>
|
|
252
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71358 71599> <>
|
|
253
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71651 71893> <>
|
|
254
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 72228 72364> <>
|
|
255
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 72409 72426> <>
|
|
256
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig18.frz3.fgene1> <>
|
|
257
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 80034 80112> <>
|
|
258
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 81258 81434> <>
|
|
259
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 81483 81700> <>
|
|
260
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82037 82188> <>
|
|
261
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82242 82536> <>
|
|
262
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82592 82854> <>
|
|
263
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83128 83210> <>
|
|
264
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83269 83375> <>
|
|
265
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83450 83570> <>
|
|
266
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83796 83872> <>
|
|
267
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83923 84129> <>
|
|
268
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84200 84265> <>
|
|
269
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84641 84792> <>
|
|
270
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84836 85080> <>
|
|
271
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 85168 85330> <>
|
|
272
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 85912 86113> <>
|
|
273
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 86152 86382> <>
|
|
274
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 86669 86825> <>
|
|
275
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 87441 87496> <>
|
|
276
|
+
WARN bio-gff3: Unknown feature is ignored <Contig>
|
|
277
|
+
INFO bio-gff3: Cache calls After reading files = 0 <>
|
|
278
|
+
INFO bio-gff3: Cache hits After reading files = 0 <>
|
|
279
|
+
INFO bio-gff3: Cache misses After reading files = 0 <>
|
|
280
|
+
WARN bio-gff3: Could not find container/component for <MhA1_Contig0.frz3.fgene1>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -60,5 +59,4 @@ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGA
|
|
|
60
59
|
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
61
60
|
INFO bio-gff3: Cache calls After iterating = 54 <>
|
|
62
61
|
INFO bio-gff3: Cache hits After iterating = 37 <>
|
|
63
|
-
INFO bio-gff3: Cache misses After iterating = 17 <>
|
|
64
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
62
|
+
INFO bio-gff3: Cache misses After iterating = 17 <>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -64,5 +63,4 @@ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
|
|
|
64
63
|
TTCATGGGC
|
|
65
64
|
INFO bio-gff3: Cache calls After iterating = 76 <>
|
|
66
65
|
INFO bio-gff3: Cache hits After iterating = 52 <>
|
|
67
|
-
INFO bio-gff3: Cache misses After iterating = 24 <>
|
|
68
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
66
|
+
INFO bio-gff3: Cache misses After iterating = 24 <>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -54,5 +53,4 @@ GAAGATTTGTAT
|
|
|
54
53
|
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTC
|
|
55
54
|
INFO bio-gff3: find_component: Matched seqname <test01>
|
|
56
55
|
>mrna01a Sequence:test01_1:400 (101:280)
|
|
57
|
-
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
58
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
56
|
+
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -58,5 +57,4 @@ GAAGATTTGTAT
|
|
|
58
57
|
TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
|
|
59
58
|
INFO bio-gff3: find_component: Matched seqname <test01>
|
|
60
59
|
>cds2 Sequence:test01_1:400 (192:200)
|
|
61
|
-
TTCATGGGC
|
|
62
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
60
|
+
TTCATGGGC
|
data/test/helper.rb
CHANGED
|
@@ -6,9 +6,9 @@
|
|
|
6
6
|
# Copyright:: July 2007
|
|
7
7
|
# License:: Ruby License
|
|
8
8
|
|
|
9
|
-
module
|
|
9
|
+
module RegressionTest2
|
|
10
10
|
|
|
11
|
-
def
|
|
11
|
+
def RegressionTest2.create b
|
|
12
12
|
@@test_create = b
|
|
13
13
|
end
|
|
14
14
|
|
|
@@ -16,12 +16,12 @@ module RegressionTest
|
|
|
16
16
|
# in test/regression with +filename+. When +create+ is +true+ the file
|
|
17
17
|
# will be created/overwritten. Otherwise it is tested against returning
|
|
18
18
|
# whether it has equal or not. When a test fails both test file and new
|
|
19
|
-
# file exist in the
|
|
19
|
+
# file exist in the regression directory - so you can execute a diff.
|
|
20
20
|
#
|
|
21
21
|
# Example:
|
|
22
|
-
#
|
|
22
|
+
# RegressionTest2.test `#{cfrubybin} --help`,'cfruby_helptext',$test_create
|
|
23
23
|
|
|
24
|
-
def
|
|
24
|
+
def RegressionTest2.test text, filename, testdir, create = @@test_create
|
|
25
25
|
fn = testdir+'/'+filename+'.rtest'
|
|
26
26
|
fntest = fn+'.new'
|
|
27
27
|
|
data/test/test_bio-gff3.rb
CHANGED
|
@@ -1,18 +1,26 @@
|
|
|
1
|
+
# To recreate the regression files:
|
|
2
|
+
#
|
|
3
|
+
# ruby -Itest test/test_bio-gff3.rb --create
|
|
4
|
+
|
|
1
5
|
$: << '.'
|
|
2
6
|
do_create = if ARGV[0] == '-c' or ARGV[0] == '--create'
|
|
3
7
|
ARGV.shift
|
|
4
8
|
end
|
|
9
|
+
|
|
10
|
+
$:.unshift "../regressiontest/lib" # override gem location, when available
|
|
5
11
|
|
|
6
12
|
require 'test/unit'
|
|
7
13
|
require 'regressiontest'
|
|
14
|
+
require 'regressiontest2'
|
|
15
|
+
|
|
16
|
+
RegressionTest2.create(do_create)
|
|
8
17
|
|
|
9
|
-
|
|
18
|
+
rootpath = File.join(File.dirname(__FILE__),'..')
|
|
19
|
+
DAT = rootpath + '/test/data'
|
|
20
|
+
BIN = rootpath + '/bin/gff3-fetch'
|
|
10
21
|
|
|
11
22
|
class Gff3Test < Test::Unit::TestCase
|
|
12
23
|
|
|
13
|
-
rootpath = File.join(File.dirname(__FILE__),'..')
|
|
14
|
-
BIN = rootpath + '/bin/gff3-fetch'
|
|
15
|
-
DAT = rootpath + '/test/data'
|
|
16
24
|
def test_cache
|
|
17
25
|
assert_equal(true,single_run("mRNA #{DAT}/gff/test-ext-fasta.fa #{DAT}/gff/test-ext-fasta.gff3",'test_ext_gff3'))
|
|
18
26
|
assert_equal(true,single_run("CDS #{DAT}/gff/test.gff3",'test_gff3'))
|
|
@@ -28,15 +36,32 @@ class Gff3Test < Test::Unit::TestCase
|
|
|
28
36
|
assert_equal(true,single_run("CDS --cache lru #{DAT}/gff/test.gff3",this_method+'_gff3'))
|
|
29
37
|
end
|
|
30
38
|
|
|
39
|
+
def test_latest_wormbase
|
|
40
|
+
opts = "CDS #{DAT}/gff/m_hapla.WS232.genomic.part.fa #{DAT}/gff/m_hapla.WS232.annotations.part.gff3"
|
|
41
|
+
arg1 = this_method + '_ext_gff3'
|
|
42
|
+
|
|
43
|
+
bin = File.expand_path(BIN)
|
|
44
|
+
cmd = "#{bin} --logger stdout #{opts}"
|
|
45
|
+
assert_equal(true,RegressionTest::CliExec::exec(cmd,arg1,:ignore => 'Memory used'))
|
|
46
|
+
end
|
|
47
|
+
|
|
31
48
|
private
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
49
|
+
|
|
50
|
+
def this_method
|
|
51
|
+
caller[0] =~ /`([^']*)'/ and $1
|
|
52
|
+
end
|
|
35
53
|
|
|
36
54
|
end
|
|
37
55
|
|
|
38
56
|
def single_run opts, name
|
|
39
|
-
|
|
40
|
-
#
|
|
41
|
-
|
|
57
|
+
bin = File.expand_path(BIN)
|
|
58
|
+
cmd = "#{bin} --logger stdout #{opts}"
|
|
59
|
+
if false
|
|
60
|
+
print "Skipping ", cmd, "!\n"
|
|
61
|
+
else
|
|
62
|
+
text = `#{cmd}`.split(/\n/).delete_if { | s | s =~ /Memory/ }.join("\n")
|
|
63
|
+
|
|
64
|
+
RegressionTest2.test text,name,"#{DAT}/regression"
|
|
65
|
+
end
|
|
66
|
+
true
|
|
42
67
|
end
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-gff3
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.9.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,11 +9,11 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date:
|
|
12
|
+
date: 2012-08-20 00:00:00.000000000Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: bio
|
|
16
|
-
requirement: &
|
|
16
|
+
requirement: &26586340 !ruby/object:Gem::Requirement
|
|
17
17
|
none: false
|
|
18
18
|
requirements:
|
|
19
19
|
- - ! '>='
|
|
@@ -21,10 +21,10 @@ dependencies:
|
|
|
21
21
|
version: 1.3.1
|
|
22
22
|
type: :runtime
|
|
23
23
|
prerelease: false
|
|
24
|
-
version_requirements: *
|
|
24
|
+
version_requirements: *26586340
|
|
25
25
|
- !ruby/object:Gem::Dependency
|
|
26
26
|
name: log4r
|
|
27
|
-
requirement: &
|
|
27
|
+
requirement: &26584780 !ruby/object:Gem::Requirement
|
|
28
28
|
none: false
|
|
29
29
|
requirements:
|
|
30
30
|
- - ! '>'
|
|
@@ -32,10 +32,10 @@ dependencies:
|
|
|
32
32
|
version: 1.1.6
|
|
33
33
|
type: :runtime
|
|
34
34
|
prerelease: false
|
|
35
|
-
version_requirements: *
|
|
35
|
+
version_requirements: *26584780
|
|
36
36
|
- !ruby/object:Gem::Dependency
|
|
37
37
|
name: bio-logger
|
|
38
|
-
requirement: &
|
|
38
|
+
requirement: &26583820 !ruby/object:Gem::Requirement
|
|
39
39
|
none: false
|
|
40
40
|
requirements:
|
|
41
41
|
- - ! '>'
|
|
@@ -43,10 +43,10 @@ dependencies:
|
|
|
43
43
|
version: 0.8.0
|
|
44
44
|
type: :runtime
|
|
45
45
|
prerelease: false
|
|
46
|
-
version_requirements: *
|
|
46
|
+
version_requirements: *26583820
|
|
47
47
|
- !ruby/object:Gem::Dependency
|
|
48
48
|
name: shoulda
|
|
49
|
-
requirement: &
|
|
49
|
+
requirement: &26581520 !ruby/object:Gem::Requirement
|
|
50
50
|
none: false
|
|
51
51
|
requirements:
|
|
52
52
|
- - ! '>='
|
|
@@ -54,51 +54,51 @@ dependencies:
|
|
|
54
54
|
version: '0'
|
|
55
55
|
type: :development
|
|
56
56
|
prerelease: false
|
|
57
|
-
version_requirements: *
|
|
57
|
+
version_requirements: *26581520
|
|
58
58
|
- !ruby/object:Gem::Dependency
|
|
59
59
|
name: bundler
|
|
60
|
-
requirement: &
|
|
60
|
+
requirement: &26579580 !ruby/object:Gem::Requirement
|
|
61
61
|
none: false
|
|
62
62
|
requirements:
|
|
63
63
|
- - ~>
|
|
64
64
|
- !ruby/object:Gem::Version
|
|
65
|
-
version: 1.
|
|
65
|
+
version: 1.1.5
|
|
66
66
|
type: :development
|
|
67
67
|
prerelease: false
|
|
68
|
-
version_requirements: *
|
|
68
|
+
version_requirements: *26579580
|
|
69
69
|
- !ruby/object:Gem::Dependency
|
|
70
70
|
name: jeweler
|
|
71
|
-
requirement: &
|
|
71
|
+
requirement: &26578680 !ruby/object:Gem::Requirement
|
|
72
72
|
none: false
|
|
73
73
|
requirements:
|
|
74
74
|
- - ~>
|
|
75
75
|
- !ruby/object:Gem::Version
|
|
76
|
-
version: 1.
|
|
76
|
+
version: 1.8.3
|
|
77
77
|
type: :development
|
|
78
78
|
prerelease: false
|
|
79
|
-
version_requirements: *
|
|
79
|
+
version_requirements: *26578680
|
|
80
80
|
- !ruby/object:Gem::Dependency
|
|
81
|
-
name:
|
|
82
|
-
requirement: &
|
|
81
|
+
name: rspec
|
|
82
|
+
requirement: &26578060 !ruby/object:Gem::Requirement
|
|
83
83
|
none: false
|
|
84
84
|
requirements:
|
|
85
85
|
- - ! '>='
|
|
86
86
|
- !ruby/object:Gem::Version
|
|
87
|
-
version:
|
|
87
|
+
version: 2.10.0
|
|
88
88
|
type: :development
|
|
89
89
|
prerelease: false
|
|
90
|
-
version_requirements: *
|
|
90
|
+
version_requirements: *26578060
|
|
91
91
|
- !ruby/object:Gem::Dependency
|
|
92
|
-
name:
|
|
93
|
-
requirement: &
|
|
92
|
+
name: regressiontest
|
|
93
|
+
requirement: &26577240 !ruby/object:Gem::Requirement
|
|
94
94
|
none: false
|
|
95
95
|
requirements:
|
|
96
96
|
- - ! '>='
|
|
97
97
|
- !ruby/object:Gem::Version
|
|
98
|
-
version:
|
|
98
|
+
version: '0'
|
|
99
99
|
type: :development
|
|
100
100
|
prerelease: false
|
|
101
|
-
version_requirements: *
|
|
101
|
+
version_requirements: *26577240
|
|
102
102
|
description: ! 'GFF3 (genome browser) information and digest mRNA and CDS sequences.
|
|
103
103
|
|
|
104
104
|
Options for low memory use and caching of records.
|
|
@@ -114,6 +114,7 @@ extra_rdoc_files:
|
|
|
114
114
|
- LICENSE.txt
|
|
115
115
|
- README.rdoc
|
|
116
116
|
files:
|
|
117
|
+
- .travis.yml
|
|
117
118
|
- Gemfile
|
|
118
119
|
- Gemfile.lock
|
|
119
120
|
- LICENSE.txt
|
|
@@ -152,6 +153,8 @@ files:
|
|
|
152
153
|
- test/data/gff/MhA1_Contig1133.gff3
|
|
153
154
|
- test/data/gff/MhA1_Contig125.fa
|
|
154
155
|
- test/data/gff/MhA1_Contig125.gff3
|
|
156
|
+
- test/data/gff/m_hapla.WS232.annotations.part.gff3
|
|
157
|
+
- test/data/gff/m_hapla.WS232.genomic.part.fa
|
|
155
158
|
- test/data/gff/standard.gff3
|
|
156
159
|
- test/data/gff/test-cds.gff3
|
|
157
160
|
- test/data/gff/test-ext-fasta.fa
|
|
@@ -159,12 +162,14 @@ files:
|
|
|
159
162
|
- test/data/gff/test.gff3
|
|
160
163
|
- test/data/regression/test_ext_gff3.rtest
|
|
161
164
|
- test/data/regression/test_gff3.rtest
|
|
165
|
+
- test/data/regression/test_latest_wormbase_ext_gff3.ref
|
|
166
|
+
- test/data/regression/test_latest_wormbase_ext_gff3.rtest
|
|
162
167
|
- test/data/regression/test_lrucache_ext_gff3.rtest
|
|
163
168
|
- test/data/regression/test_lrucache_gff3.rtest
|
|
164
169
|
- test/data/regression/test_nocache_ext_gff3.rtest
|
|
165
170
|
- test/data/regression/test_nocache_gff3.rtest
|
|
166
171
|
- test/helper.rb
|
|
167
|
-
- test/
|
|
172
|
+
- test/regressiontest2.rb
|
|
168
173
|
- test/test_bio-gff3.rb
|
|
169
174
|
homepage: https://github.com/pjotrp/bioruby-gff3-plugin
|
|
170
175
|
licenses:
|
|
@@ -179,6 +184,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
179
184
|
- - ! '>='
|
|
180
185
|
- !ruby/object:Gem::Version
|
|
181
186
|
version: '0'
|
|
187
|
+
segments:
|
|
188
|
+
- 0
|
|
189
|
+
hash: -3577199160742117809
|
|
182
190
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
183
191
|
none: false
|
|
184
192
|
requirements:
|
|
@@ -187,17 +195,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
187
195
|
version: '0'
|
|
188
196
|
requirements: []
|
|
189
197
|
rubyforge_project:
|
|
190
|
-
rubygems_version: 1.8.
|
|
198
|
+
rubygems_version: 1.8.10
|
|
191
199
|
signing_key:
|
|
192
200
|
specification_version: 3
|
|
193
201
|
summary: GFF3 parser for big data
|
|
194
|
-
test_files:
|
|
195
|
-
- spec/gff3_assemble2_spec.rb
|
|
196
|
-
- spec/gff3_assemble3_spec.rb
|
|
197
|
-
- spec/gff3_assemble_spec.rb
|
|
198
|
-
- spec/gff3_fileiterator_spec.rb
|
|
199
|
-
- spec/gffdb_spec.rb
|
|
200
|
-
- spec/gffparserec.rb
|
|
201
|
-
- test/helper.rb
|
|
202
|
-
- test/regressiontest.rb
|
|
203
|
-
- test/test_bio-gff3.rb
|
|
202
|
+
test_files: []
|