| Previous changeset 2:326f9c294b09 (2019-05-03) Next changeset 4:e408aa831db3 (2021-01-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" |
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modified:
macros.xml test-data/annot_human.gff3 test-data/annot_model.gff3 test-data/evidences_human.gff3 test-data/evidences_model.gff3 test-data/evidences_norm.gff3 test-data/evidences_reuse.gff3 |
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added:
test-data/Dfam_partial_test.h5 test-data/annot_dfam.gff3 test-data/annot_dfam_up.gff3 test-data/evidences_norm_dfam_up.gff3 |
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removed:
test-data/annot_repbase.gff3 |
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| diff -r 326f9c294b09 -r f1912d5575df macros.xml --- a/macros.xml Fri May 03 07:50:37 2019 -0400 +++ b/macros.xml Mon Dec 28 23:19:28 2020 +0000 |
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| @@ -6,7 +6,7 @@ <yield /> </requirements> </xml> - <token name="@VERSION@">2.31.10</token> + <token name="@VERSION@">2.31.11</token> <xml name="citations"> <citations> |
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| diff -r 326f9c294b09 -r f1912d5575df test-data/Dfam_partial_test.h5 |
| b |
| Binary file test-data/Dfam_partial_test.h5 has changed |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/annot_dfam.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_dfam.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| @@ -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 +### +### |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/annot_dfam_up.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_dfam_up.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| @@ -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 +### +### |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/annot_human.gff3 --- a/test-data/annot_human.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/annot_human.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -1,44 +1,42 @@\n ##gff-version 3\n-HS08198\tmaker\tgene\t352\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4;Name=maker-HS08198-augustus-gene-0.4\n-HS08198\tmaker\tmRNA\t352\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1;Parent=maker-HS08198-augustus-gene-0.4;Name=maker-HS08198-augustus-gene-0.4-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0.83|0.85|7|0|192\n-HS08198\tmaker\texon\t352\t397\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:10;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t421\t582\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:11;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t812\t894\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:12;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t1053\t1123\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:13;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t1208\t1315\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:14;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t1587\t1688\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:15;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\texon\t1772\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:16;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tfive_prime_UTR\t352\t397\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tfive_prime_UTR\t421\t444\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t445\t582\t.\t+\t0\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t812\t894\t.\t+\t0\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t1053\t1123\t.\t+\t1\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t1208\t1315\t.\t+\t2\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t1587\t1688\t.\t+\t2\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-HS08198\tmaker\tCDS\t1772\t1848\t.\t+\t2\tID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1\n-###\n+HS08198\tmaker\tgene\t352\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1;Name=maker-HS08198-augustus-gene-0.1\n+HS08198\tmaker\tmRNA\t352\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1;Parent=maker-HS08198-augustus-gene-0.1;Name=maker-HS08198-augustus-gene-0.1-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0.83|0.85|7|0|192\n+HS08198\tmaker\texon\t352\t397\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:10;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t421\t582\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:11;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t812\t894\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:12;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t1053\t1123\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:13;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t1208\t1315\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:14;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t1587\t1688\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:15;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\texon\t1772\t1848\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:16;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\tfive_prime_UTR\t352\t397\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\tfive_prime_UTR\t421\t444\t.\t+\t.\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker\tCDS\t445\t582\t.\t+\t0\tID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1\n+HS08198\tmaker'..b'augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t2055\t2198\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t2852\t2995\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t3426\t3607\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t4340\t4423\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t4543\t4789\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t5072\t5358\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t5860\t6007\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n-HS04636\tmaker\tCDS\t6494\t6903\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1\n+HS04636\tmaker\tgene\t966\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3;Name=maker-HS04636-augustus-gene-0.3\n+HS04636\tmaker\tmRNA\t966\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1;Parent=maker-HS04636-augustus-gene-0.3;Name=maker-HS04636-augustus-gene-0.3-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.88|0.8|0.9|1|1|10|0|604\n+HS04636\tmaker\texon\t966\t1017\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t1818\t1934\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t2055\t2198\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t2852\t2995\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t3426\t3607\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t4340\t4423\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t4543\t4789\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t5072\t5358\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t5860\t6007\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\texon\t6494\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:9;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t966\t1017\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t1818\t1934\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t2055\t2198\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t2852\t2995\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t3426\t3607\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t4340\t4423\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t4543\t4789\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t5072\t5358\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t5860\t6007\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n+HS04636\tmaker\tCDS\t6494\t6903\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1\n ###\n-###\n' |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/annot_model.gff3 --- a/test-data/annot_model.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/annot_model.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -1,41 +1,40 @@\n ##gff-version 3\n-HS08198\tmaker\tgene\t352\t1848\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0\n-HS08198\tmaker\tmRNA\t352\t1848\t2869\t+\t.\tID=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\n-HS08198\tmaker\texon\t352\t397\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t421\t582\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t812\t894\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t1053\t1123\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t1208\t1315\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t1587\t1688\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\texon\t1772\t1848\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tfive_prime_UTR\t352\t397\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tfive_prime_UTR\t421\t444\t.\t+\t.\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t445\t582\t.\t+\t0\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t812\t894\t.\t+\t0\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t1053\t1123\t.\t+\t1\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t1208\t1315\t.\t+\t2\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t1587\t1688\t.\t+\t2\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n-HS08198\tmaker\tCDS\t1772\t1848\t.\t+\t2\tID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1\n+HS08198\tmaker\tgene\t99\t1848\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3;Name=maker-HS08198-snap-gene-0.3\n+HS08198\tmaker\tmRNA\t99\t1848\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1;Parent=maker-HS08198-snap-gene-0.3;Name=maker-HS08198-snap-gene-0.3-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|0.66|0.57|0.85|0.83|0.85|7|0|190\n+HS08198\tmaker\texon\t99\t107\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:9;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t421\t582\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:10;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t812\t874\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:11;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t1072\t1123\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:12;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t1208\t1315\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:13;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t1587\t1688\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:14;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\texon\t1772\t1848\t.\t+\t.\tID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:15;Parent=maker-HS08198-snap-gene-0.3-mRNA-1\n+HS08198\tmaker\tCDS\t99\t107\t.\t+\t0\tID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198'..b'-HS04636\tmaker\tCDS\t2055\t2198\t.\t+\t2\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t2852\t2995\t.\t+\t2\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t3426\t3607\t.\t+\t2\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t4340\t4423\t.\t+\t0\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t4543\t4789\t.\t+\t0\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t5072\t5358\t.\t+\t2\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t5860\t6007\t.\t+\t0\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n-HS04636\tmaker\tCDS\t6494\t6903\t.\t+\t2\tID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1\n+HS04636\tmaker\tgene\t1813\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0;Name=maker-HS04636-augustus-gene-0.0\n+HS04636\tmaker\tmRNA\t1813\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1;Parent=maker-HS04636-augustus-gene-0.0;Name=maker-HS04636-augustus-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|1|1|9|0|572\n+HS04636\tmaker\texon\t1813\t1934\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t2055\t2198\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t2852\t2995\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t3426\t3607\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t4340\t4423\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t4543\t4789\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t5072\t5358\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t5860\t6007\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\texon\t6494\t6903\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tfive_prime_UTR\t1813\t1861\t.\t+\t.\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t1862\t1934\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t2055\t2198\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t2852\t2995\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t3426\t3607\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t4340\t4423\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t4543\t4789\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t5072\t5358\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t5860\t6007\t.\t+\t0\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n+HS04636\tmaker\tCDS\t6494\t6903\t.\t+\t2\tID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1\n ###\n' |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/annot_repbase.gff3 --- a/test-data/annot_repbase.gff3 Fri May 03 07:50:37 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,43 +0,0 @@ -##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 -### -### |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_human.gff3 --- a/test-data/evidences_human.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/evidences_human.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -1,99 +1,79 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n-HS08198\taugustus_masked\tmatch\t445\t1848\t1\t+\t.\tID=HS08198:hit:15:4.5.0.0;Name=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1\n-HS08198\taugustus_masked\tmatch_part\t445\t582\t1\t+\t.\tID=HS08198:hsp:62:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 1 138 +;Gap=M138\n-HS08198\taugustus_masked\tmatch_part\t812\t894\t1\t+\t.\tID=HS08198:hsp:63:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 139 221 +;Gap=M83\n-HS08198\taugustus_masked\tmatch_part\t1053\t1123\t1\t+\t.\tID=HS08198:hsp:64:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 222 292 +;Gap=M71\n-HS08198\taugustus_masked\tmatch_part\t1208\t1315\t1\t+\t.\tID=HS08198:hsp:65:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 293 400 +;Gap=M108\n-HS08198\taugustus_masked\tmatch_part\t1587\t1688\t1\t+\t.\tID=HS08198:hsp:66:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 401 502 +;Gap=M102\n-HS08198\taugustus_masked\tmatch_part\t1772\t1848\t1\t+\t.\tID=HS08198:hsp:67:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 503 579 +;Gap=M77\n-HS08198\tsnap_masked\tmatch\t99\t1848\t233.121\t+\t.\tID=HS08198:hit:16:4.5.0.0;Name=snap_masked-HS08198-abinit-gene-0.1-mRNA-1\n-HS08198\tsnap_masked\tmatch_part\t99\t107\t-2.800\t+\t.\tID=HS08198:hsp:68:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 1 9 +;Gap=M9\n-HS08198\tsnap_masked\tmatch_part\t421\t582\t45.298\t+\t.\tID=HS08198:hsp:69:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 10 171 +;Gap=M162\n-HS08198\tsnap_masked\tmatch_part\t812\t874\t24.711\t+\t.\tID=HS08198:hsp:70:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 172 234 +;Gap=M63\n-HS08198\tsnap_masked\tmatch_part\t1024\t1123\t34.281\t+\t.\tID=HS08198:hsp:71:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 235 334 +;Gap=M100\n-HS08198\tsnap_masked\tmatch_part\t1208\t1315\t53.852\t+\t.\tID=HS08198:hsp:72:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 335 442 +;Gap=M108\n-HS08198\tsnap_masked\tmatch_part\t1587\t1688\t41.983\t+\t.\tID=HS08198:hsp:73:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 443 544 +;Gap=M102\n-HS08198\tsnap_masked\tmatch_part\t1772\t1848\t35.796\t+\t.\tID=HS08198:hsp:74:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 545 621 +;Gap=M77\n+HS08198\taugustus\tmatch\t445\t1848\t1\t+\t.\tID=HS08198:hit:6:4.5.0.0;Name=augustus-HS08198-abinit-gene-0.2-mRNA-1\n+HS08198\taugustus\tmatch_part\t445\t582\t1\t+\t.\tID=HS08198:hsp:53:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 1 138 +;Gap=M138\n+HS08198\taugustus\tmatch_part\t812\t894\t1\t+\t.\tID=HS08198:hsp:54:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 139 221 +;Gap=M83\n+HS08198\taugustus\tmatch_part\t1053\t1123\t1\t+\t.\tID=HS08198:hsp:55:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 222 292 +;Gap=M71\n+HS08198\taugustus\tmatch_part\t1208\t1315\t1\t+\t.\tID=HS08198:hsp:56:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 293 400 +;Gap=M108\n+HS08198\taugustus\tmatch_part\t1587\t1688\t1\t+\t.\tID=HS08198:hsp:57:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 401 502 +;Gap=M102\n+HS08198\taugustus\tmatch_part\t1772\t1848\t1\t+\t.\tID=HS08198:hsp:58:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 503 579 +;Gap=M77\n+HS08198\tsnap\tmatch\t99\t1848\t233.121\t+\t.\tID=HS08198:hit:7:4.5.0.0;Name=snap-HS08198-abinit-gene-0.4-mRNA-1\n+HS08198\tsnap\tmatch_part\t99\t107\t-2.800\t+\t.\tID=HS08198:hsp:59:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 1 9 +;Gap=M9\n+'..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 326f9c294b09 -r f1912d5575df test-data/evidences_model.gff3 --- a/test-data/evidences_model.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/evidences_model.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -1,23 +1,51 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n+HS08198\tsnap\tmatch\t99\t1848\t233.121\t+\t.\tID=HS08198:hit:6:4.5.0.0;Name=snap-HS08198-abinit-gene-0.0-mRNA-1\n+HS08198\tsnap\tmatch_part\t99\t107\t-2.800\t+\t.\tID=HS08198:hsp:51:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 1 9 +;Gap=M9\n+HS08198\tsnap\tmatch_part\t421\t582\t45.298\t+\t.\tID=HS08198:hsp:52:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 10 171 +;Gap=M162\n+HS08198\tsnap\tmatch_part\t812\t874\t24.711\t+\t.\tID=HS08198:hsp:53:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 172 234 +;Gap=M63\n+HS08198\tsnap\tmatch_part\t1024\t1123\t34.281\t+\t.\tID=HS08198:hsp:54:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 235 334 +;Gap=M100\n+HS08198\tsnap\tmatch_part\t1208\t1315\t53.852\t+\t.\tID=HS08198:hsp:55:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 335 442 +;Gap=M108\n+HS08198\tsnap\tmatch_part\t1587\t1688\t41.983\t+\t.\tID=HS08198:hsp:56:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 443 544 +;Gap=M102\n+HS08198\tsnap\tmatch_part\t1772\t1848\t35.796\t+\t.\tID=HS08198:hsp:57:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 545 621 +;Gap=M77\n ###\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;Parent=HS08198:hit:3:3.2.0.0;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:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:4:3.2.0.0;Name=HS08198.g2\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\t'..b'04636-abinit-gene-0.2-mRNA-1 59 202 +;Gap=M144\n+HS04636\tsnap\tmatch_part\t2852\t2995\t67.055\t+\t.\tID=HS04636:hsp:22:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 203 346 +;Gap=M144\n+HS04636\tsnap\tmatch_part\t3426\t3607\t77.942\t+\t.\tID=HS04636:hsp:23:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 347 528 +;Gap=M182\n+HS04636\tsnap\tmatch_part\t4340\t4423\t47.588\t+\t.\tID=HS04636:hsp:24:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 529 612 +;Gap=M84\n+HS04636\tsnap\tmatch_part\t4543\t4789\t112.472\t+\t.\tID=HS04636:hsp:25:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 613 859 +;Gap=M247\n+HS04636\tsnap\tmatch_part\t5072\t5358\t122.974\t+\t.\tID=HS04636:hsp:26:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 860 1146 +;Gap=M287\n+HS04636\tsnap\tmatch_part\t5860\t6007\t72.046\t+\t.\tID=HS04636:hsp:27:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 1147 1294 +;Gap=M148\n+HS04636\tsnap\tmatch_part\t6494\t6903\t163.122\t+\t.\tID=HS04636:hsp:28:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 1295 1704 +;Gap=M410\n+HS04636\taugustus\tmatch\t966\t6903\t0.1\t+\t.\tID=HS04636:hit:3:4.5.0.0;Name=augustus-HS04636-abinit-gene-0.3-mRNA-1\n+HS04636\taugustus\tmatch_part\t966\t1017\t0.1\t+\t.\tID=HS04636:hsp:29:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 1 52 +;Gap=M52\n+HS04636\taugustus\tmatch_part\t2852\t2995\t0.1\t+\t.\tID=HS04636:hsp:30:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 53 196 +;Gap=M144\n+HS04636\taugustus\tmatch_part\t3426\t3607\t0.1\t+\t.\tID=HS04636:hsp:31:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 197 378 +;Gap=M182\n+HS04636\taugustus\tmatch_part\t4340\t4423\t0.1\t+\t.\tID=HS04636:hsp:32:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 379 462 +;Gap=M84\n+HS04636\taugustus\tmatch_part\t4543\t4789\t0.1\t+\t.\tID=HS04636:hsp:33:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 463 709 +;Gap=M247\n+HS04636\taugustus\tmatch_part\t5072\t5358\t0.1\t+\t.\tID=HS04636:hsp:34:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 710 996 +;Gap=M287\n+HS04636\taugustus\tmatch_part\t5860\t6007\t0.1\t+\t.\tID=HS04636:hsp:35:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 997 1144 +;Gap=M148\n+HS04636\taugustus\tmatch_part\t6494\t6903\t0.1\t+\t.\tID=HS04636:hsp:36:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 1145 1554 +;Gap=M410\n ###\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@@ -26,7 +54,7 @@\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\t4541\t4790\t250\t+\t.\tID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250\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' |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_norm.gff3 --- a/test-data/evidences_norm.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/evidences_norm.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -1,42 +1,66 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n ###\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;Parent=HS08198:hit:3:3.2.0.0;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:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\trepeatmasker\tmatch\t578\t651\t13\t+\t.\tID=HS08198:hit:12:1.3.0.0;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:29:1.3.0.0;Parent=HS08198:hit:12:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +\n+###\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:13:3.2.0.0;Name=HS08198.g2\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n+HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n+HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n+HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:14:3.2.0.0;Name=HS08198.g2\n+HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;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:38:3.2.0.0;Parent=H'..b'%29n|genus:Simple_repeat 1 24 +\n+HS04636\trepeatmasker\tmatch_part\t4518\t4541\t17\t+\t.\tID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +\n+HS04636\trepeatmasker\tmatch\t1124\t1335\t391\t+\t.\tID=HS04636:hit:7:1.3.0.0;Name=species:MIRb|genus:SINE%2FMIR;Target=species:MIRb|genus:SINE%2FMIR 2 217 +\n+HS04636\trepeatmasker\tmatch_part\t1124\t1335\t391\t+\t.\tID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:MIRb|genus:SINE%252FMIR 2 217 +\n+HS04636\trepeatmasker\tmatch\t6050\t6359\t2256\t+\t.\tID=HS04636:hit:8:1.3.0.0;Name=species:AluSc8|genus:SINE%2FAlu;Target=species:AluSc8|genus:SINE%2FAlu 1 311 +\n+HS04636\trepeatmasker\tmatch_part\t6050\t6359\t2256\t+\t.\tID=HS04636:hsp:8:1.3.0.0;Parent=HS04636:hit:8:1.3.0.0;Target=species:AluSc8|genus:SINE%252FAlu 1 311 +\n+HS04636\trepeatmasker\tmatch\t8994\t9045\t191\t+\t.\tID=HS04636:hit:9:1.3.0.0;Name=species:L2a|genus:LINE%2FL2;Target=species:L2a|genus:LINE%2FL2 3374 3425 +\n+HS04636\trepeatmasker\tmatch_part\t8994\t9045\t191\t+\t.\tID=HS04636:hsp:9:1.3.0.0;Parent=HS04636:hit:9:1.3.0.0;Target=species:L2a|genus:LINE%252FL2 3374 3425 +\n+###\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:10:3.2.0.0;Name=HS04636.g1\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4541\t4790\t250\t+\t.\tID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t5999\t141\t+\t.\tID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1336 1476 +;Gap=M141\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:11:3.2.0.0;Name=HS04636.g1\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:27:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:28:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n' |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_norm_dfam_up.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_norm_dfam_up.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| b'@@ -0,0 +1,62 @@\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+HS04636\t.\tcontig\t1\t9453\t.\t.\t.\tID=HS04636;Name=HS04636\n+###\n+HS04636\trepeatmasker\tmatch\t6918\t6977\t17\t+\t.\tID=HS04636:hit:0:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +\n+HS04636\trepeatmasker\tmatch_part\t6918\t6977\t17\t+\t.\tID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +\n+HS04636\trepeatmasker\tmatch\t939\t980\t13\t+\t.\tID=HS04636:hit:1:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +\n+HS04636\trepeatmasker\tmatch_part\t939\t980\t13\t+\t.\tID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +\n+HS04636\trepeatmasker\tmatch\t3791\t3839\t22\t+\t.\tID=HS04636:hit:2:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +\n+HS04636\trepeatmasker\tmatch_part\t3791\t3839\t22\t+\t.\tID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +\n+HS04636\trepeatmasker\tmatch\t4518\t4541\t17\t+\t.\tID=HS04636:hit:3:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +\n+HS04636\trepeatmasker\tmatch_part\t4518\t4541\t17\t+\t.\tID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +\n'..b'er\tmatch_part\t3840\t3847\t17\t+\t.\tID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +\n+HS04636\trepeatmasker\tmatch\t3852\t3888\t12\t+\t.\tID=HS04636:hit:5:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +\n+HS04636\trepeatmasker\tmatch_part\t3852\t3888\t12\t+\t.\tID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +\n+HS04636\trepeatmasker\tmatch\t6028\t6072\t21\t+\t.\tID=HS04636:hit:6:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +\n+HS04636\trepeatmasker\tmatch_part\t6028\t6072\t21\t+\t.\tID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +\n+HS04636\trepeatmasker\tmatch\t9419\t9435\t16\t+\t.\tID=HS04636:hit:7:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +\n+HS04636\trepeatmasker\tmatch_part\t9419\t9435\t16\t+\t.\tID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +\n+###\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4541\t4790\t250\t+\t.\tID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t6008\t150\t+\t.\tID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=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' |
| b |
| diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_reuse.gff3 --- a/test-data/evidences_reuse.gff3 Fri May 03 07:50:37 2019 -0400 +++ b/test-data/evidences_reuse.gff3 Mon Dec 28 23:19:28 2020 +0000 |
| b |
| @@ -26,7 +26,7 @@ HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:3:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146 HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:4:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186 HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:5:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85 -HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 4542 4790 249 + . ID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 802 1050 +;Gap=M249 HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:7:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 |