Mercurial > repos > iuc > maker_map_ids
changeset 0:060ea7339911 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
| author | iuc |
|---|---|
| date | Thu, 19 Oct 2017 15:59:20 -0400 |
| parents | |
| children | 1b3626164087 |
| files | macros.xml map_ids.xml test-data/annot.gff3 test-data/annot_human.gff3 test-data/annot_mapped.gff3 test-data/annot_model.gff3 test-data/annot_norm.gff3 test-data/annot_proc.gff3 test-data/annot_reuse.gff3 test-data/est.fasta test-data/evidences.gff3 test-data/evidences_human.gff3 test-data/evidences_model.gff3 test-data/evidences_norm.gff3 test-data/evidences_proc.gff3 test-data/evidences_reuse.gff3 test-data/genome.fasta test-data/id_map.tsv test-data/local.tar.gz test-data/snap.hmm |
| diffstat | 20 files changed, 2477 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,17 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">maker</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">2.31.9</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1002/0471250953.bi0411s48</citation> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/map_ids.xml Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<tool id="maker_map_ids" name="Map annotation ids" profile="16.04" version="@VERSION@"> + <description>on a Maker annotation</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + cp '${maker_gff}' '${renamed}' && + maker_map_ids --prefix '${prefix}' --justify ${justify} '${maker_gff}' > '${id_map}' && + map_gff_ids '${id_map}' '${renamed}' + ]]></command> + <inputs> + <param name="maker_gff" type="data" format="gff" label="Maker annotation where to change ids"/> + <param name="prefix" type="text" label="Prefix for ids"/> + <param name="justify" type="integer" value="6" min="2" max="20" label="Justify numeric ids to this length"/> + </inputs> + <outputs> + <data format="gff" name="renamed" label="${tool.name} on ${on_string}: renamed GFF"/> + <data format="tabular" name="id_map" label="${tool.name} on ${on_string}: ID map"/> + </outputs> + <tests> + <test> + <param name="maker_gff" value="annot.gff3"/> + <param name="prefix" value="YES"/> + <param name="justify" value="6"/> + <output name="renamed" file="annot_mapped.gff3"/> + <output name="id_map" file="id_map.tsv"/> + </test> + </tests> + <help><![CDATA[ + MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. + + This tool will automatically assign new ids to a Maker annotation respecting a specified pattern. + + .. _Maker: http://www.yandell-lab.org/software/maker.html + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -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 +### +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_human.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,44 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-augustus-gene-0.4;Name=maker-HS08198-augustus-gene-0.4 +HS08198 maker mRNA 352 1848 . + . ID=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 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:10;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:11;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:12;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:13;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:14;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:15;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:16;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1 +### +### +HS04636 maker gene 966 6903 . + . ID=maker-HS04636-augustus-gene-0.4;Name=maker-HS04636-augustus-gene-0.4 +HS04636 maker mRNA 966 6903 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1;Parent=maker-HS04636-augustus-gene-0.4;Name=maker-HS04636-augustus-gene-0.4-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.88|0.8|0.9|1|1|10|0|604 +HS04636 maker exon 966 1017 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 1818 1934 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:9;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 966 1017 . + 0 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 1818 1934 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1 +### +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_mapped.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,43 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=YES000002;Name=YES000002;Alias=maker-HS08198-exonerate_est2genome-gene-0.0; +HS08198 maker mRNA 352 1848 2869 + . ID=YES000002-RA;Parent=YES000002;Name=YES000002-RA;Alias=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=70|1|1|1|0|0|7|0|192;_eAED=0.00; +HS08198 maker exon 352 397 . + . ID=YES000002-RA:exon:9;Parent=YES000002-RA; +HS08198 maker exon 421 582 . + . ID=YES000002-RA:exon:10;Parent=YES000002-RA; +HS08198 maker exon 812 894 . + . ID=YES000002-RA:exon:11;Parent=YES000002-RA; +HS08198 maker exon 1053 1123 . + . ID=YES000002-RA:exon:12;Parent=YES000002-RA; +HS08198 maker exon 1208 1315 . + . ID=YES000002-RA:exon:13;Parent=YES000002-RA; +HS08198 maker exon 1587 1688 . + . ID=YES000002-RA:exon:14;Parent=YES000002-RA; +HS08198 maker exon 1772 1848 . + . ID=YES000002-RA:exon:15;Parent=YES000002-RA; +HS08198 maker five_prime_UTR 352 397 . + . ID=YES000002-RA:five_prime_utr;Parent=YES000002-RA; +HS08198 maker five_prime_UTR 421 444 . + . ID=YES000002-RA:five_prime_utr;Parent=YES000002-RA; +HS08198 maker CDS 445 582 . + 0 ID=YES000002-RA:cds;Parent=YES000002-RA; +HS08198 maker CDS 812 894 . + 0 ID=YES000002-RA:cds;Parent=YES000002-RA; +HS08198 maker CDS 1053 1123 . + 1 ID=YES000002-RA:cds;Parent=YES000002-RA; +HS08198 maker CDS 1208 1315 . + 2 ID=YES000002-RA:cds;Parent=YES000002-RA; +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; +HS04636 maker exon 2055 2198 . + . ID=YES000001-RA:exon:1;Parent=YES000001-RA; +HS04636 maker exon 2852 2995 . + . ID=YES000001-RA:exon:2;Parent=YES000001-RA; +HS04636 maker exon 3426 3607 . + . ID=YES000001-RA:exon:3;Parent=YES000001-RA; +HS04636 maker exon 4340 4423 . + . ID=YES000001-RA:exon:4;Parent=YES000001-RA; +HS04636 maker exon 4543 4789 . + . ID=YES000001-RA:exon:5;Parent=YES000001-RA; +HS04636 maker exon 5072 5358 . + . ID=YES000001-RA:exon:6;Parent=YES000001-RA; +HS04636 maker exon 5860 6007 . + . ID=YES000001-RA:exon:7;Parent=YES000001-RA; +HS04636 maker exon 6494 6903 . + . ID=YES000001-RA:exon:8;Parent=YES000001-RA; +HS04636 maker five_prime_UTR 1813 1861 . + . ID=YES000001-RA:five_prime_utr;Parent=YES000001-RA; +HS04636 maker CDS 1862 1934 . + 0 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 2055 2198 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 2852 2995 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 3426 3607 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 4340 4423 . + 0 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 4543 4789 . + 0 ID=YES000001-RA:cds;Parent=YES000001-RA; +HS04636 maker CDS 5072 5358 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; +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; +### +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_model.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,41 @@ +##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 +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_norm.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,41 @@ +##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 +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_proc.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,3 @@ +##gff-version 3 +### +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_reuse.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,43 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-est2genome-gene-0.0;Name=maker-HS08198-est2genome-gene-0.0;score=2869 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-est2genome-gene-0.0;Name=maker-HS08198-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-est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 +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 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 +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 +### +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/est.fasta Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,35 @@ +>HS04636.g1 +atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca +tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa +aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg +ctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccact +tcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatca +catttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatta +tactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattcaa +atgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattcttt +gcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggt +ggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatc +agataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag +catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggga +acacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa +tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaattt +gacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggca +tccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattgc +tggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcca +cccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaa +acgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactct +atggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaacc +atggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaag +cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct +gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga +ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag +>HS08198.g2 +atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca +tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc +cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc +caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg +tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg +gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc +ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga +tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca +agcatggcggcgtggtga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,62 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +### +HS08198 repeatmasker match 578 651 13 + . ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 + +HS08198 repeatmasker match_part 578 651 13 + . ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 + +### +HS08198 blastn expressed_sequence_match 444 1848 140 + . ID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2 +HS08198 blastn match_part 444 583 140 + . ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140 +HS08198 blastn match_part 445 523 79 + . ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79 +HS08198 blastn match_part 808 895 88 + . ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88 +HS08198 blastn match_part 1053 1123 71 + . ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 blastn match_part 1206 1315 110 + . ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110 +HS08198 blastn match_part 1586 1689 104 + . ID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104 +HS08198 blastn match_part 1771 1848 78 + . ID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78 +HS08198 est2genome expressed_sequence_match 352 1848 2869 + . ID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2 +HS08198 est2genome match_part 352 397 2869 + . ID=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 +HS08198 est2genome match_part 421 582 2869 + . ID=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 +HS08198 est2genome match_part 812 894 2869 + . ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83 +HS08198 est2genome match_part 1053 1123 2869 + . ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 est2genome match_part 1208 1315 2869 + . ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108 +HS08198 est2genome match_part 1587 1688 2869 + . ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102 +HS08198 est2genome match_part 1772 1848 2869 + . ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77 +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +### +HS04636 repeatmasker match 9419 9435 16 + . ID=HS04636:hit:0:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 + +HS04636 repeatmasker match_part 9419 9435 16 + . ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 + +HS04636 repeatmasker match 939 980 13 + . ID=HS04636:hit:1:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match_part 939 980 13 + . ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match 3791 3839 22 + . ID=HS04636:hit:2:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match_part 3791 3839 22 + . ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match 6918 6977 17 + . ID=HS04636:hit:3:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match_part 6918 6977 17 + . ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match 6028 6072 21 + . ID=HS04636:hit:4:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match_part 6028 6072 21 + . ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match 4518 4541 17 + . ID=HS04636:hit:5:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 + +HS04636 repeatmasker match_part 4518 4541 17 + . ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 + +HS04636 repeatmasker match 3852 3888 12 + . ID=HS04636:hit:6:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match_part 3852 3888 12 + . ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match 3840 3847 17 + . ID=HS04636:hit:7:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 + +HS04636 repeatmasker match_part 3840 3847 17 + . ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 + +### +HS04636 blastn expressed_sequence_match 1815 6903 120 + . ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1 +HS04636 blastn match_part 1815 1934 120 + . ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120 +HS04636 blastn match_part 1815 1845 31 + . ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31 +HS04636 blastn match_part 2055 2198 144 + . ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146 +HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186 +HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85 +HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 +HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 +HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 +HS04636 est2genome expressed_sequence_match 1813 6903 8728 + . ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1 +HS04636 est2genome match_part 1813 1934 8728 + . ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122 +HS04636 est2genome match_part 2055 2198 8728 + . ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 est2genome match_part 2852 2995 8728 + . ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144 +HS04636 est2genome match_part 3426 3607 8728 + . ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182 +HS04636 est2genome match_part 4340 4423 8728 + . ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84 +HS04636 est2genome match_part 4543 4789 8728 + . ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247 +HS04636 est2genome match_part 5072 5358 8728 + . ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287 +HS04636 est2genome match_part 5860 6007 8728 + . ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148 +HS04636 est2genome match_part 6494 6903 8728 + . ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_human.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,99 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +HS08198 augustus_masked match 445 1848 1 + . ID=HS08198:hit:15:4.5.0.0;Name=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 +HS08198 augustus_masked match_part 445 582 1 + . ID=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 +HS08198 augustus_masked match_part 812 894 1 + . ID=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 +HS08198 augustus_masked match_part 1053 1123 1 + . ID=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 +HS08198 augustus_masked match_part 1208 1315 1 + . ID=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 +HS08198 augustus_masked match_part 1587 1688 1 + . ID=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 +HS08198 augustus_masked match_part 1772 1848 1 + . ID=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 +HS08198 snap_masked match 99 1848 233.121 + . ID=HS08198:hit:16:4.5.0.0;Name=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 +HS08198 snap_masked match_part 99 107 -2.800 + . ID=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 +HS08198 snap_masked match_part 421 582 45.298 + . ID=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 +HS08198 snap_masked match_part 812 874 24.711 + . ID=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 +HS08198 snap_masked match_part 1024 1123 34.281 + . ID=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 +HS08198 snap_masked match_part 1208 1315 53.852 + . ID=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 +HS08198 snap_masked match_part 1587 1688 41.983 + . ID=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 +HS08198 snap_masked match_part 1772 1848 35.796 + . ID=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 +### +HS08198 repeatmasker match 578 651 13 + . ID=HS08198:hit:12:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 + +HS08198 repeatmasker match_part 578 651 13 + . ID=HS08198:hsp:47:1.3.0.0;Parent=HS08198:hit:12:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 + +### +HS08198 blastn expressed_sequence_match 444 1848 140 + . ID=HS08198:hit:13:3.2.0.0;Name=HS08198.g2 +HS08198 blastn match_part 444 583 140 + . ID=HS08198:hsp:48:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140 +HS08198 blastn match_part 445 523 79 + . ID=HS08198:hsp:49:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79 +HS08198 blastn match_part 808 895 88 + . ID=HS08198:hsp:50:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88 +HS08198 blastn match_part 1053 1123 71 + . ID=HS08198:hsp:51:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 blastn match_part 1206 1315 110 + . ID=HS08198:hsp:52:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110 +HS08198 blastn match_part 1586 1689 104 + . ID=HS08198:hsp:53:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104 +HS08198 blastn match_part 1771 1848 78 + . ID=HS08198:hsp:54:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78 +HS08198 est2genome expressed_sequence_match 352 1848 2869 + . ID=HS08198:hit:14:3.2.0.0;Name=HS08198.g2 +HS08198 est2genome match_part 352 397 2869 + . ID=HS08198:hsp:55:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15 +HS08198 est2genome match_part 421 582 2869 + . ID=HS08198:hsp:56:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139 +HS08198 est2genome match_part 812 894 2869 + . ID=HS08198:hsp:57:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83 +HS08198 est2genome match_part 1053 1123 2869 + . ID=HS08198:hsp:58:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 est2genome match_part 1208 1315 2869 + . ID=HS08198:hsp:59:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108 +HS08198 est2genome match_part 1587 1688 2869 + . ID=HS08198:hsp:60:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102 +HS08198 est2genome match_part 1772 1848 2869 + . ID=HS08198:hsp:61:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77 +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +HS04636 augustus_masked match 966 6903 1 + . ID=HS04636:hit:10:4.5.0.0;Name=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 +HS04636 augustus_masked match_part 966 1017 1 + . ID=HS04636:hsp:27:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1 52 +;Gap=M52 +HS04636 augustus_masked match_part 1818 1934 1 + . ID=HS04636:hsp:28:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 53 169 +;Gap=M117 +HS04636 augustus_masked match_part 2055 2198 1 + . ID=HS04636:hsp:29:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 170 313 +;Gap=M144 +HS04636 augustus_masked match_part 2852 2995 1 + . ID=HS04636:hsp:30:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 314 457 +;Gap=M144 +HS04636 augustus_masked match_part 3426 3607 1 + . ID=HS04636:hsp:31:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 458 639 +;Gap=M182 +HS04636 augustus_masked match_part 4340 4423 1 + . ID=HS04636:hsp:32:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 640 723 +;Gap=M84 +HS04636 augustus_masked match_part 4543 4789 1 + . ID=HS04636:hsp:33:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 724 970 +;Gap=M247 +HS04636 augustus_masked match_part 5072 5358 1 + . ID=HS04636:hsp:34:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 971 1257 +;Gap=M287 +HS04636 augustus_masked match_part 5860 6007 1 + . ID=HS04636:hsp:35:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1258 1405 +;Gap=M148 +HS04636 augustus_masked match_part 6494 6903 1 + . ID=HS04636:hsp:36:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1406 1815 +;Gap=M410 +HS04636 snap_masked match 1862 6903 761.916 + . ID=HS04636:hit:11:4.5.0.0;Name=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 +HS04636 snap_masked match_part 1862 1867 8.523 + . ID=HS04636:hsp:37:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1 6 +;Gap=M6 +HS04636 snap_masked match_part 1883 1934 20.348 + . ID=HS04636:hsp:38:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 7 58 +;Gap=M52 +HS04636 snap_masked match_part 2055 2198 69.846 + . ID=HS04636:hsp:39:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 59 202 +;Gap=M144 +HS04636 snap_masked match_part 2852 2995 67.055 + . ID=HS04636:hsp:40:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 203 346 +;Gap=M144 +HS04636 snap_masked match_part 3426 3607 77.942 + . ID=HS04636:hsp:41:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 347 528 +;Gap=M182 +HS04636 snap_masked match_part 4340 4423 47.588 + . ID=HS04636:hsp:42:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 529 612 +;Gap=M84 +HS04636 snap_masked match_part 4543 4789 112.472 + . ID=HS04636:hsp:43:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 613 859 +;Gap=M247 +HS04636 snap_masked match_part 5072 5358 122.974 + . ID=HS04636:hsp:44:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 860 1146 +;Gap=M287 +HS04636 snap_masked match_part 5860 6007 72.046 + . ID=HS04636:hsp:45:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1147 1294 +;Gap=M148 +HS04636 snap_masked match_part 6494 6903 163.122 + . ID=HS04636:hsp:46:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1295 1704 +;Gap=M410 +### +HS04636 repeatmasker match 3852 3888 12 + . ID=HS04636:hit:0:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match_part 3852 3888 12 + . ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match 4518 4541 17 + . ID=HS04636:hit:1:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 + +HS04636 repeatmasker match_part 4518 4541 17 + . ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 + +HS04636 repeatmasker match 939 980 13 + . ID=HS04636:hit:2:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match_part 939 980 13 + . ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match 3791 3839 22 + . ID=HS04636:hit:3:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match_part 3791 3839 22 + . ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match 6028 6072 21 + . ID=HS04636:hit:4:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match_part 6028 6072 21 + . ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match 6918 6977 17 + . ID=HS04636:hit:5:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match_part 6918 6977 17 + . ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match 3840 3847 17 + . ID=HS04636:hit:6:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 + +HS04636 repeatmasker match_part 3840 3847 17 + . ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 + +HS04636 repeatmasker match 9419 9435 16 + . ID=HS04636:hit:7:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 + +HS04636 repeatmasker match_part 9419 9435 16 + . ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 + +### +HS04636 blastn expressed_sequence_match 1815 6903 120 + . ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1 +HS04636 blastn match_part 1815 1934 120 + . ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120 +HS04636 blastn match_part 1815 1845 31 + . ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31 +HS04636 blastn match_part 2055 2198 144 + . ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146 +HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186 +HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85 +HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 +HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 +HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 +HS04636 est2genome expressed_sequence_match 1813 6903 8728 + . ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1 +HS04636 est2genome match_part 1813 1934 8728 + . ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122 +HS04636 est2genome match_part 2055 2198 8728 + . ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 est2genome match_part 2852 2995 8728 + . ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144 +HS04636 est2genome match_part 3426 3607 8728 + . ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182 +HS04636 est2genome match_part 4340 4423 8728 + . ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84 +HS04636 est2genome match_part 4543 4789 8728 + . ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247 +HS04636 est2genome match_part 5072 5358 8728 + . ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287 +HS04636 est2genome match_part 5860 6007 8728 + . ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148 +HS04636 est2genome match_part 6494 6903 8728 + . ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_model.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,42 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +### +HS08198 blastn expressed_sequence_match 444 1848 140 + . ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2 +HS08198 blastn match_part 444 583 140 + . ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140 +HS08198 blastn match_part 445 523 79 + . ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79 +HS08198 blastn match_part 808 895 88 + . ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88 +HS08198 blastn match_part 1053 1123 71 + . ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 blastn match_part 1206 1315 110 + . ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110 +HS08198 blastn match_part 1586 1689 104 + . ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104 +HS08198 blastn match_part 1771 1848 78 + . ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78 +HS08198 est2genome expressed_sequence_match 352 1848 2869 + . ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2 +HS08198 est2genome match_part 352 397 2869 + . ID=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 +HS08198 est2genome match_part 421 582 2869 + . ID=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 +HS08198 est2genome match_part 812 894 2869 + . ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83 +HS08198 est2genome match_part 1053 1123 2869 + . ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 est2genome match_part 1208 1315 2869 + . ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108 +HS08198 est2genome match_part 1587 1688 2869 + . ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102 +HS08198 est2genome match_part 1772 1848 2869 + . ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77 +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +### +HS04636 blastn expressed_sequence_match 1815 6903 120 + . ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1 +HS04636 blastn match_part 1815 1934 120 + . ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120 +HS04636 blastn match_part 1815 1845 31 + . ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31 +HS04636 blastn match_part 2055 2198 144 + . ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146 +HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186 +HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85 +HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 +HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 +HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 +HS04636 est2genome expressed_sequence_match 1813 6903 8728 + . ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1 +HS04636 est2genome match_part 1813 1934 8728 + . ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122 +HS04636 est2genome match_part 2055 2198 8728 + . ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 est2genome match_part 2852 2995 8728 + . ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144 +HS04636 est2genome match_part 3426 3607 8728 + . ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182 +HS04636 est2genome match_part 4340 4423 8728 + . ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84 +HS04636 est2genome match_part 4543 4789 8728 + . ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247 +HS04636 est2genome match_part 5072 5358 8728 + . ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287 +HS04636 est2genome match_part 5860 6007 8728 + . ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148 +HS04636 est2genome match_part 6494 6903 8728 + . ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_norm.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,42 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +### +HS08198 blastn expressed_sequence_match 444 1848 140 + . ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2 +HS08198 blastn match_part 444 583 140 + . ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140 +HS08198 blastn match_part 445 523 79 + . ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79 +HS08198 blastn match_part 808 895 88 + . ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88 +HS08198 blastn match_part 1053 1123 71 + . ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 blastn match_part 1206 1315 110 + . ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110 +HS08198 blastn match_part 1586 1689 104 + . ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104 +HS08198 blastn match_part 1771 1848 78 + . ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78 +HS08198 est2genome expressed_sequence_match 352 1848 2869 + . ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2 +HS08198 est2genome match_part 352 397 2869 + . ID=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 +HS08198 est2genome match_part 421 582 2869 + . ID=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 +HS08198 est2genome match_part 812 894 2869 + . ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83 +HS08198 est2genome match_part 1053 1123 2869 + . ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 est2genome match_part 1208 1315 2869 + . ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108 +HS08198 est2genome match_part 1587 1688 2869 + . ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102 +HS08198 est2genome match_part 1772 1848 2869 + . ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77 +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +### +HS04636 blastn expressed_sequence_match 1815 6903 120 + . ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1 +HS04636 blastn match_part 1815 1934 120 + . ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120 +HS04636 blastn match_part 1815 1845 31 + . ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31 +HS04636 blastn match_part 2055 2198 144 + . ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146 +HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186 +HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85 +HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 +HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 +HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 +HS04636 est2genome expressed_sequence_match 1813 6903 8728 + . ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1 +HS04636 est2genome match_part 1813 1934 8728 + . ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122 +HS04636 est2genome match_part 2055 2198 8728 + . ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 est2genome match_part 2852 2995 8728 + . ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144 +HS04636 est2genome match_part 3426 3607 8728 + . ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182 +HS04636 est2genome match_part 4340 4423 8728 + . ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84 +HS04636 est2genome match_part 4543 4789 8728 + . ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247 +HS04636 est2genome match_part 5072 5358 8728 + . ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287 +HS04636 est2genome match_part 5860 6007 8728 + . ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148 +HS04636 est2genome match_part 6494 6903 8728 + . ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_proc.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,5 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +### +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidences_reuse.gff3 Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,62 @@ +##gff-version 3 +HS08198 . contig 1 2344 . . . ID=HS08198;Name=HS08198 +### +HS08198 repeatmasker match 578 651 13 + . ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 + +HS08198 repeatmasker match_part 578 651 13 + . ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 + +### +HS08198 blastn expressed_sequence_match 444 1848 140 + . ID=HS08198:hit:11:3.12.0.0;Name=HS08198.g2;score=140 +HS08198 blastn match_part 444 583 140 + . ID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140 +HS08198 blastn match_part 445 523 79 + . ID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79 +HS08198 blastn match_part 808 895 88 + . ID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88 +HS08198 blastn match_part 1053 1123 71 + . ID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 blastn match_part 1206 1315 110 + . ID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110 +HS08198 blastn match_part 1586 1689 104 + . ID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104 +HS08198 blastn match_part 1771 1848 78 + . ID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78 +HS08198 est2genome expressed_sequence_match 352 1848 2869 + . ID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869 +HS08198 est2genome match_part 352 397 2869 + . ID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46 +HS08198 est2genome match_part 421 582 2869 + . ID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162 +HS08198 est2genome match_part 812 894 2869 + . ID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83 +HS08198 est2genome match_part 1053 1123 2869 + . ID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71 +HS08198 est2genome match_part 1208 1315 2869 + . ID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108 +HS08198 est2genome match_part 1587 1688 2869 + . ID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102 +HS08198 est2genome match_part 1772 1848 2869 + . ID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77 +HS04636 . contig 1 9453 . . . ID=HS04636;Name=HS04636 +### +HS04636 repeatmasker match 3852 3888 12 + . ID=HS04636:hit:0:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match_part 3852 3888 12 + . ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 + +HS04636 repeatmasker match 6028 6072 21 + . ID=HS04636:hit:1:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match_part 6028 6072 21 + . ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 + +HS04636 repeatmasker match 3840 3847 17 + . ID=HS04636:hit:2:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 + +HS04636 repeatmasker match_part 3840 3847 17 + . ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 + +HS04636 repeatmasker match 3791 3839 22 + . ID=HS04636:hit:3:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match_part 3791 3839 22 + . ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 + +HS04636 repeatmasker match 9419 9435 16 + . ID=HS04636:hit:4:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 + +HS04636 repeatmasker match_part 9419 9435 16 + . ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 + +HS04636 repeatmasker match 939 980 13 + . ID=HS04636:hit:5:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match_part 939 980 13 + . ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 + +HS04636 repeatmasker match 6918 6977 17 + . ID=HS04636:hit:6:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match_part 6918 6977 17 + . ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 + +HS04636 repeatmasker match 4518 4541 17 + . ID=HS04636:hit:7:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 + +HS04636 repeatmasker match_part 4518 4541 17 + . ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 + +### +HS04636 blastn expressed_sequence_match 1815 6903 120 + . ID=HS04636:hit:8:3.12.0.0;Name=HS04636.g1;score=120 +HS04636 blastn match_part 1815 1934 120 + . ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120 +HS04636 blastn match_part 1815 1845 31 + . ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31 +HS04636 blastn match_part 2055 2198 144 + . ID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 blastn match_part 2852 2997 146 + . ID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146 +HS04636 blastn match_part 3424 3609 186 + . ID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186 +HS04636 blastn match_part 4339 4423 85 + . ID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85 +HS04636 blastn match_part 4541 4790 250 + . ID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250 +HS04636 blastn match_part 5068 5360 293 + . ID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293 +HS04636 blastn match_part 5859 6008 150 + . ID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150 +HS04636 blastn match_part 6490 6903 414 + . ID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414 +HS04636 est2genome expressed_sequence_match 1813 6903 8728 + . ID=HS04636:hit:9:3.12.0.0;Name=HS04636.g1;score=8728 +HS04636 est2genome match_part 1813 1934 8728 + . ID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122 +HS04636 est2genome match_part 2055 2198 8728 + . ID=HS04636:hsp:19:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144 +HS04636 est2genome match_part 2852 2995 8728 + . ID=HS04636:hsp:20:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144 +HS04636 est2genome match_part 3426 3607 8728 + . ID=HS04636:hsp:21:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182 +HS04636 est2genome match_part 4340 4423 8728 + . ID=HS04636:hsp:22:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84 +HS04636 est2genome match_part 4543 4789 8728 + . ID=HS04636:hsp:23:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247 +HS04636 est2genome match_part 5072 5358 8728 + . ID=HS04636:hsp:24:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287 +HS04636 est2genome match_part 5860 6007 8728 + . ID=HS04636:hsp:25:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148 +HS04636 est2genome match_part 6494 6903 8728 + . ID=HS04636:hsp:26:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Thu Oct 19 15:59:20 2017 -0400 @@ -0,0 +1,200 @@ +>HS04636 +gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta +cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt +cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc +tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag +agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta +accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac +cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct +cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc +gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca +tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga +caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat +tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg +ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac +atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca 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