bio-gff3 0.6.0
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- data/Gemfile +14 -0
- data/Gemfile.lock +22 -0
- data/LICENSE.txt +20 -0
- data/README +65 -0
- data/README.rdoc +19 -0
- data/Rakefile +56 -0
- data/VERSION +1 -0
- data/bin/gff3-fetch +99 -0
- data/bio-gff3.gemspec +101 -0
- data/lib/bio-gff3.rb +0 -0
- data/lib/bio/db/gff/gffassemble.rb +300 -0
- data/lib/bio/db/gff/gffdb.rb +40 -0
- data/lib/bio/db/gff/gfffasta.rb +68 -0
- data/lib/bio/db/gff/gfffileiterator.rb +77 -0
- data/lib/bio/db/gff/gffinmemory.rb +63 -0
- data/lib/bio/db/gff/gffnocache.rb +124 -0
- data/lib/bio/db/gff/gffparser.rb +154 -0
- data/lib/bio/system/lruhash.rb +268 -0
- data/spec/gff3_assemble2_spec.rb +73 -0
- data/spec/gff3_assemble3_spec.rb +62 -0
- data/spec/gff3_assemble_spec.rb +291 -0
- data/spec/gff3_fileiterator_spec.rb +43 -0
- data/spec/gffdb_spec.rb +99 -0
- data/test/data/gff/MhA1_Contig1133.fa +2 -0
- data/test/data/gff/MhA1_Contig1133.gff3 +1862 -0
- data/test/data/gff/MhA1_Contig125.fa +673 -0
- data/test/data/gff/MhA1_Contig125.gff3 +2177 -0
- data/test/data/gff/standard.gff3 +25 -0
- data/test/data/gff/test-cds.gff3 +98 -0
- data/test/data/gff/test-ext-fasta.fa +16 -0
- data/test/data/gff/test-ext-fasta.gff3 +57 -0
- data/test/data/gff/test.gff3 +74 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-gff3.rb +7 -0
- metadata +180 -0
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1
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##gff-version 3 ##sequence-region
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2
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+
ctg123 1 1497228
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3
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+
ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
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4
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+
ctg123 . TF_binding_site 1000 1012 . + . Parent=gene00001
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5
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+
ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001
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6
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+
ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001
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7
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+
ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001
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8
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+
ctg123 . exon 1300 1500 . + . Parent=mRNA00003
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9
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+
ctg123 . exon 1050 1500 . + . Parent=mRNA00001,mRNA00002
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10
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+
ctg123 . exon 3000 3902 . + . Parent=mRNA00001,mRNA00003
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11
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+
ctg123 . exon 5000 5500 . + . Parent=mRNA00001,mRNA00002,mRNA00003
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12
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+
ctg123 . exon 7000 9000 . + . Parent=mRNA00001,mRNA00002,mRNA00003
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13
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+
ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001
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14
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+
ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001
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15
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+
ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001
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16
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+
ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001
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17
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+
ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002
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18
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+
ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002
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19
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+
ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002
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20
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+
ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003
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21
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+
ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003
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22
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+
ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003
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23
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+
ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003
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24
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+
ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003
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25
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+
ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003
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1
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##gff-version 3 ##sequence-regio
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2
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# Gene gene:MhA1_Contig1040.frz3.gene29
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3
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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
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4
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+
MhA1_Contig1040 WormBase mRNA 1 182 . - . ID=transcript:MhA1_Contig1040.
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5
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frz3.gene29;Parent=gene:MhA1_Contig1040.frz3.gene29;Name=MhA1_Contig1040.frz3.ge
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6
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+
ne29;public_name=MhA1_Contig1040.frz3.gene29
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7
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MhA1_Contig1040 WormBase exon 1 182 . - . ID=exon:MhA1_Contig1040.frz3.g
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8
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ene29.1;Parent=transcript:MhA1_Contig1040.frz3.gene29
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9
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+
MhA1_Contig1040 WormBase CDS 1 180 . - 2 ID=cds:MhA1_Contig1040.frz3.gene
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10
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+
29;Parent=transcript:MhA1_Contig1040.frz3.gene29
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11
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+
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12
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##gff-version 3 ##sequence-regio
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13
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# Gene gene:MhA1_Contig2992.frz3.gene1
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14
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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
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15
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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
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16
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MhA1_Contig2992 WormBase exon 2078 2176 . - . ID=exon:MhA1_Contig2992.frz3.gene1.1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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17
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MhA1_Contig2992 WormBase exon 1692 1944 . - . ID=exon:MhA1_Contig2992.frz3.gene1.2;Parent=transcript:MhA1_Contig2992.frz3.gene1
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18
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MhA1_Contig2992 WormBase exon 1439 1587 . - . ID=exon:MhA1_Contig2992.frz3.gene1.3;Parent=transcript:MhA1_Contig2992.frz3.gene1
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19
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MhA1_Contig2992 WormBase exon 1096 1241 . - . ID=exon:MhA1_Contig2992.frz3.gene1.4;Parent=transcript:MhA1_Contig2992.frz3.gene1
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20
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MhA1_Contig2992 WormBase exon 927 1049 . - . ID=exon:MhA1_Contig2992.frz3.gene1.5;Parent=transcript:MhA1_Contig2992.frz3.gene1
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21
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MhA1_Contig2992 WormBase exon 577 732 . - . ID=exon:MhA1_Contig2992.frz3.gene1.6;Parent=transcript:MhA1_Contig2992.frz3.gene1
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22
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MhA1_Contig2992 WormBase CDS 2078 2174 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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23
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MhA1_Contig2992 WormBase CDS 1692 1944 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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24
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MhA1_Contig2992 WormBase CDS 1439 1587 . - 1 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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25
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MhA1_Contig2992 WormBase CDS 1096 1241 . - 2 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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26
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MhA1_Contig2992 WormBase CDS 927 1049 . - 0 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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27
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MhA1_Contig2992 WormBase CDS 577 732 . - 0 ID=cds:MhA1_Contig2992.frz3.gene1;Parent=transcript:MhA1_Contig2992.frz3.gene1
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28
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MhA1_Contig2992 blat_nembase_ests nucleotide_match 1778 2214 45.29 - . ID=blat_nembase_ests.1828564;Name=MJC03471;Target=MJC03471 88 372;Gap=30M29D31I66M165D11I27M18I33M19D22I10M21D37M
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29
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+
MhA1_Contig2992 blat_washu_ests nucleotide_match 1529 2164 36.82 - . ID=blat_washu_ests.2375120;Name=MJ04126;Target=MJ04126 159 530;Gap=80M159D5I24M56D77I12M21D38M3I48M131D18I67M
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30
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MhA1_Contig2992 blat_washu_ests nucleotide_match 1778 2214 34.08 - . ID=blat_washu_ests.2425103;Name=MJ04126;Target=MJ04126 106 391;Gap=59M3I66M165D11I27M18I33M19D22I10M21D37M
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31
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+
MhA1_Contig2992 TRF repeat_region 83 147 102 - . ID=TRF.57974
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32
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+
MhA1_Contig2992 RepeatMask repeat_region 169 404 2011 - . ID=RepeatMask.324631
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33
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+
MhA1_Contig2992 Dust repeat_region 397 405 . - . ID=Dust.42101
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34
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+
MhA1_Contig2992 RepeatMask repeat_region 405 565 35 + . ID=RepeatMask.324632
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35
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+
MhA1_Contig2992 Dust repeat_region 493 565 . - . ID=Dust.42102
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36
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+
MhA1_Contig2992 RepeatMask repeat_region 1243 1266 24 + . ID=RepeatMask.324633
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37
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+
MhA1_Contig2992 RepeatMask repeat_region 1695 1834 200 + . ID=RepeatMask.324634
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38
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+
MhA1_Contig2992 Dust repeat_region 1709 1795 . - . ID=Dust.42103
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39
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+
MhA1_Contig2992 Dust repeat_region 1881 1931 . - . ID=Dust.42104
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40
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+
MhA1_Contig2992 Dust repeat_region 1944 2071 . - . ID=Dust.42105
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41
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+
MhA1_Contig2992 RepeatMask repeat_region 1946 2076 45 + . ID=RepeatMask.324635
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42
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+
MhA1_Contig2992 RepeatMask repeat_region 2136 2257 66 + . ID=RepeatMask.324636
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43
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+
MhA1_Contig2992 Dust repeat_region 2159 2281 . - . ID=Dust.42107
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44
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+
MhA1_Contig2992 TRF repeat_region 2305 2364 76 - . ID=TRF.57978
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45
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+
MhA1_Contig2992 Dust repeat_region 2319 2380 . - . ID=Dust.42109
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46
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+
MhA1_Contig2992 RepeatMask repeat_region 2333 2437 42 + . ID=RepeatMask.324637
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47
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+
MhA1_Contig2992 Dust repeat_region 2395 2437 . - . ID=Dust.42110
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48
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+
MhA1_Contig2992 TRF repeat_region 2688 2730 56 - . ID=TRF.57984
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49
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+
MhA1_Contig2992 RepeatMask repeat_region 2957 3019 28 + . ID=RepeatMask.324638
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50
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+
MhA1_Contig2992 Dust repeat_region 2959 3019 . - . ID=Dust.42112
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51
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MhA1_Contig2992 RepeatMask repeat_region 3194 3237 23 + . ID=RepeatMask.324639
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52
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MhA1_Contig2992 Dust repeat_region 3222 3277 . - . ID=Dust.42114
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53
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##FASTA
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54
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>MhA1_Contig2992
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55
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TTTTGGTGACCAAAGTTCCTATTGGTGACCAAAATTCCAGTGCCCAATATTCCGTTTTTTGACTTGGTGACCAAAATTCC
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56
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+
GCTGGTGACCAAAATTCCAAAAAATTGGTGACCAAAGTTCCGAAAAATCTTGGTGACCAAAATTCCGGTGACCAAAATTC
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57
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+
TGGGACTCCTCAGGTTCGATGCCTGGCGGCAGCTGGTGGCCGGTTTAGTGTAGTCCCTGTATAGCACTTACACAGGTGGC
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58
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+
ACGCCCTGAGTGGGGAGGCAATTGGGTCTAGCGTGCTTGTAAATACCGAGCCGGCAAAAGGTATTGACACATCCACTAAC
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59
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+
AAGTATATGTAAATCCTTAACACTCCCCCTCCACATGTAAGTGCCTAAAAGCCTCTGTGGTTGATTTAATTACACCAAAA
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60
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AAAAATTATAAATTTTATTTTCTTAAACTTTTGTTTTATGATTTAATTAATTTATAACACATCATATTATTTAACCAGTT
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61
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TTCATAATTAGTAAATAATTTTTCATTCAATAAATTTCATGTAATTTAGAAATAAGAAAAATTTTAAAAAATTATAATTT
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62
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+
AAAAACGATTATTATTCTATGTAAGATTTGGCGGTATATTTCCATCTAATGGTCCAATAACAGATATTTGTCTTTGTAAT
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63
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+
TCCTGACGAATACTATCGTCTGTACCGCCGAGGATTTGTTCAATTTGAAGAATTAAAGCTCTTTCAGCAATATCAGGATT
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64
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ATTCAGAAGATCCTTTAAACTTTGAATTATTTGTAAATAAATGTAGGGATACTAAATTATTTTTATTAAATAGAGTTATT
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65
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TTACAGAAAAATATTCTATGAGGCAAAATAAAAGCAATATTTATTATTAAACTATCAAGCAATAAATTCTTTCCTTGACG
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66
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+
AAAATTTTTGACTTAAAAAAATCAGGCCTTAACAATTAATTATTACCTGAATTCTTTTATCAACATTCTGTGCATTTCTG
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67
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+
CTTAATTTAATTTGAACATTTCGTTGACGTTCACTTTTAAATTGTTTTTCTTTTTGTTGTAAAGATTGTTGAAATTGTTT
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68
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+
ATAAAGATCCTCAAAATAGAACAAATTTAATTGTTAACTCTAAAAATAAACAAACAGAAATTCTCTGCCCTTGTTGATCA
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69
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+
GCCCAATTCTGTTTATCTCTTCGTATAGAAGACTTGGACCTGTCATTTTCTGCTTCAAGTTGAAGAAATTTCTGACGCTC
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70
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+
TGAGAGACTGGCCGTTTTCAAAAATTCTGGTAATTGATCATCTAAATAAAATTTAAATATTAATTTGTTTCAACATTTAT
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71
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+
CCTTATATTTCTCAAATTTTCATTTAAATAACTTTCTTAATTCCAGATAACCCCAAATTTGTAATGTCTTTGTCATTCGA
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72
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+
CATAGAAAAACGAATCCATAAATTGGGCGAAGGATCCTTAAAATTTTCACGCCACGAAAATAAAAATATAAAGATTACCA
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73
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+
TTCGATCTTTTTAAATTATTTGTTCCATCTAATGTGCCGCTATCTAAGCCTCTTTGTGATTTATCATTATTGCCAGAATC
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74
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AAAACTATCACGTTGATTATTTCTGTCTTGATTCTGCTCATCAAACCTTTCAGAAGCCTTATTTCTTCTAAATTGTTAAA
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75
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TATTGAAATACTTTTTCGATCTCTAAGTATTATCGAAAATTAAAATATACAGTGATTTATTATAATAAAAGAACATAATT
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76
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+
TGATAACATACTCATTTTTATCCCTTCCTTTATTCCTTCCTAATTCATACTTTTCTATCATTCCTTTTTTCCCTTTCTTT
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77
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+
TTTCTATTATCCTCTTCTTTTTCATATTCACTTTCATTATCCCCAAAATTACTTATTTGTTTTTTGCTTTCTTTTGAAGG
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78
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+
TATTTCATTATTATCAAAACCTTCACTTTGAATATCCAACTCTTTATTTCCTTCTTTTTGATTTTTACCGAATTTTTTGT
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79
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+
TGCCTTTTTTTGTTGCTATATTGTCTAAATAAAATAATGTTAAAATCTAATTTAAATGTTAAAATTTAATTTGTGATTTT
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80
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+
TTTCAATTTTCGGCTTATAAAAATCTTTTTTTAAAAAACAAAATTTTAATTAAATAAGTTTTAATAAAAATATTTACCTT
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81
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+
CATTTTGTTCAGAATTAATTCCATCATTAAACAAATTTTCATTCGAATCAGATTGAATATTAAAAGAATTATCATTTATT
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82
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+
TTTTTATTAATTTTAGCTTTGATAATTAATAAATAAAAAGTAAATAATAATAATTTTATTAATATTTTCATATTAATTTT
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83
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+
AGAATTTTATTTATTTTGACAGTTAATAAGTATTATTATTAGAAAACTTGCCAATAATTGATTTCTAAATTTAAATGGAT
|
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84
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+
TTTTGTTTCAGCTAAATTTAAATGTTTTATTTCATTTAAATTTAGAAATTTATTATGTTTGTATAGCATTATTCAATAAT
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85
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+
TTTTAATAAATAAATTTAAATTTTTTGAATAAAAAATCGAGAAAACCTAAATTATATATTAAGAATTTCTAAATTTCTCG
|
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86
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+
AAGATATTTACAAAACAACTTGCAAAGTGATATTTTTTCTAAACATGTCAAAAGCCCTAATTATTACATGCATTAAAGCA
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87
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+
AAAATTTTCTTTTTAATATTTGAAATAAATTCCAATCAAAGGATTTACGATAATCAAGAAATAATATAGTTCATATATTC
|
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88
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+
TAATAAAGTCTTTAATATAATATACCTAGTCTTTAGAAGTAGAATTCAGAAAAGTTTATAAAGAAGAGAAATAGTTTAAA
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89
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+
GGAAAGAAAAAATCATTCAAAAATTGTTTTCTTATCATATATTCTTTACATCTTTTGAAGTTTGTGTATAAACCAAATTG
|
|
90
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+
TAGAATATATTGAAAATAAAATCACTCCAATAATAATTAACAAAATACATAAAAAATGGCGTGGTTGACAACCGCATTTT
|
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91
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+
CTCTCAATATCGAAGCCACGTTTGCGGCGATTTTTATTTTGAAGAGGAAAATCTGATATTTATTGTATAGATTTAGTTAT
|
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92
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+
TTAATAATTAAATTTCAAAAATTACTTGTCTTATTTAATCTTTTATTTATTTTATTTTTGCATTCAAAAGAAGGAATCTC
|
|
93
|
+
AAATTTTAAAGTAAATGCTTTCCAAATTGAAATAGCCATATCAAAAGATCCTTCATTTATTAAAGGTTCTTTTCTCACAA
|
|
94
|
+
TAATATTCTCCATTTCTTTCCAATCAAAATTATTCTTTATTTCAAAACTATTCCAAAAATTATCCAAAATTCCAATTAAA
|
|
95
|
+
TATTTTTTGTTAAATAAAAGGTTTAAATTAATTATTTGTGCTTTTTCGAATTTTTCATTTAAATCCTTTATTTTTTTGAA
|
|
96
|
+
ATTATCATAAAGCTCTAATGATGCTTTTTGAATTTTTGAGACATTTTCAATATCAAAATTTGGTCCGGAAAATTTATTTA
|
|
97
|
+
>MhA1_Contig1040
|
|
98
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+
TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAAAC
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1
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>test01
|
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2
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ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
|
|
3
|
+
GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
|
|
4
|
+
CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
|
|
5
|
+
AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
6
|
+
GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
|
|
7
|
+
CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
|
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8
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+
>test02
|
|
9
|
+
ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
|
|
10
|
+
GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
|
|
11
|
+
CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
|
|
12
|
+
AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
13
|
+
GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
|
|
14
|
+
CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
|
|
15
|
+
|
|
16
|
+
|
|
@@ -0,0 +1,57 @@
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1
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##gff-version 3
|
|
2
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+
## 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
|
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6
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+
Contig1 confirmed exon 1401 1450 . + . ID=Transcript:trans-1
|
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7
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+
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
|
|
@@ -0,0 +1,74 @@
|
|
|
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
|
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
|