| Previous changeset 0:060ea7339911 (2017-10-19) Next changeset 2:326f9c294b09 (2019-05-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 |
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modified:
test-data/annot.gff3 test-data/annot_mapped.gff3 test-data/annot_reuse.gff3 test-data/evidences.gff3 test-data/evidences_reuse.gff3 |
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added:
test-data/annot_repbase.gff3 test-data/fake_repbase.embl |
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| diff -r 060ea7339911 -r 1b3626164087 test-data/annot.gff3 --- a/test-data/annot.gff3 Thu Oct 19 15:59:20 2017 -0400 +++ b/test-data/annot.gff3 Sun Jul 01 16:12:07 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 ### -### HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 ### -### |
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| diff -r 060ea7339911 -r 1b3626164087 test-data/annot_mapped.gff3 --- a/test-data/annot_mapped.gff3 Thu Oct 19 15:59:20 2017 -0400 +++ b/test-data/annot_mapped.gff3 Sun Jul 01 16:12:07 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=YES000002-RA:cds;Parent=YES000002-RA; HS08198 maker CDS 1772 1848 . + 2 ID=YES000002-RA:cds;Parent=YES000002-RA; ### -### HS04636 maker gene 1813 6903 . + . ID=YES000001;Name=YES000001;Alias=maker-HS04636-exonerate_est2genome-gene-0.0; HS04636 maker mRNA 1813 6903 8728 + . ID=YES000001-RA;Parent=YES000001;Name=YES000001-RA;Alias=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=49|1|1|1|0|0|9|0|572;_eAED=0.00; HS04636 maker exon 1813 1934 . + . ID=YES000001-RA:exon:0;Parent=YES000001-RA; @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=YES000001-RA:cds;Parent=YES000001-RA; HS04636 maker CDS 6494 6903 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; ### -### |
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| diff -r 060ea7339911 -r 1b3626164087 test-data/annot_repbase.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_repbase.gff3 Sun Jul 01 16:12:07 2018 -0400 |
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| @@ -0,0 +1,43 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +### +### +HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 +HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 +HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +### +### |
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| diff -r 060ea7339911 -r 1b3626164087 test-data/annot_reuse.gff3 --- a/test-data/annot_reuse.gff3 Thu Oct 19 15:59:20 2017 -0400 +++ b/test-data/annot_reuse.gff3 Sun Jul 01 16:12:07 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 ### -### HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0;score=8728 HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 ### -### |
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| diff -r 060ea7339911 -r 1b3626164087 test-data/evidences.gff3 --- a/test-data/evidences.gff3 Thu Oct 19 15:59:20 2017 -0400 +++ b/test-data/evidences.gff3 Sun Jul 01 16:12:07 2018 -0400 |
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| b'@@ -1,62 +1,42 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n ###\n-HS08198\trepeatmasker\tmatch\t578\t651\t13\t+\t.\tID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +\n-HS08198\trepeatmasker\tmatch_part\t578\t651\t13\t+\t.\tID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +\n-###\n-HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2\n-HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n-HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n-HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n-HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n-HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n-HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n-HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2\n-HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15\n-HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139\n-HS08198\test2genome\tmatch_part\t812\t894\t2869\t+\t.\tID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n+HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n+HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n+HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2\n+HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15\n+HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:27:3.2.0.0;Pa'..b'p=M122\n-HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n-HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n-HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n-HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n-HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n-HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4542\t4790\t249\t+\t.\tID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t6008\t150\t+\t.\tID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n' |
| b |
| diff -r 060ea7339911 -r 1b3626164087 test-data/evidences_reuse.gff3 --- a/test-data/evidences_reuse.gff3 Thu Oct 19 15:59:20 2017 -0400 +++ b/test-data/evidences_reuse.gff3 Sun Jul 01 16:12:07 2018 -0400 |
| b |
| b'@@ -1,62 +1,42 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n ###\n-HS08198\trepeatmasker\tmatch\t578\t651\t13\t+\t.\tID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +\n-HS08198\trepeatmasker\tmatch_part\t578\t651\t13\t+\t.\tID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +\n-###\n-HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:11:3.12.0.0;Name=HS08198.g2;score=140\n-HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n-HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n-HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n-HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n-HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n-HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n-HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869\n-HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46\n-HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162\n-HS08198\test2genome\tmatch_part\t812\t894\t2869\t+\t.\tID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:2:3.12.0.0;Name=HS08198.g2;score=140\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:19:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:20:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:21:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:22:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:23:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n+HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:24:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n+HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:25:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n+HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:3:3.12.0.0;Name=HS08198.g2;score=2869\n+HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:26:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46\n+HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID'..b'12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:20:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:21:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n-HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:22:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n-HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:23:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n-HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:24:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n-HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:25:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n-HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:26:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:0:3.12.0.0;Name=HS04636.g1;score=120\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:0:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:1:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:2:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:3:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:4:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:5:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4541\t4790\t250\t+\t.\tID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:7:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t6008\t150\t+\t.\tID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:1:3.12.0.0;Name=HS04636.g1;score=8728\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n' |
| b |
| diff -r 060ea7339911 -r 1b3626164087 test-data/fake_repbase.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_repbase.embl Sun Jul 01 16:12:07 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ +CC Fake repbase-like embl file, using data from DfamConsensus.embl* +CC **************************************************************** +XX +ID ACROBAT1 repeatmasker; DNA; ???; 768 BP. +CC consensus - See RepBase for additional annotations. +XX +SQ Sequence 768 BP; 178 A; 194 C; 215 G; 181 T; 0 other; + ggtgatgctg ccaacttact gatttagtgt atgatggtgt ttttgaggtg ctccagtggc 60 + ttctgtttct atcagctgtc cctcctgttc agctactgac ggggtggtgc gtaacggcaa 120 + aagcaccgcc ggacatcagc gctatctctg ctctcactgc cgtaaaacat ggcaactgca 180 + gttcacttac accgcttctc aacccggtac gcaccagaaa atcattgata tggccatgaa 240 + tggcgttgga tgccgggcaa cagcccgcat tatgggcgtt ggcctcaaca cgattttacg 300 + tcacttaaaa aactcaggcc gcagtcggta acctcgcgca tacagccggg cagtgacgtc 360 + atcgtctgcg cggaaatgga cgaacagtgg ggctatgtcg gggctaaatc gcgccagcgc 420 + tggctgtttt acgcgtatga cagtctccgg aagacggttg ttgcgcacgt attcggtgaa 480 + cgcactatgg cgacgctggg gcgtcttatg agcctgctgt caccctttga cgtggtgata 540 + tggatgacgg atggctggcc gctgtatgaa tcccgcctga agggaaagct gcacgtaatc 600 + agcaagcgat atacgcagcg aattgagcgg cataacctga atctgaggca gcacctggca 660 + cggctgggac ggaagtcgct gtcgttctca aaatcggtgg agctgcatga caaagtcatc 720 + gggcattatc tgaacataaa acactatcaa taagttggag tcattacc 768 +// |