Galaxy |

Changeset 5:5201ec38c01f (2020-12-28)

Previous changeset 4:5e96efe6e6c6 (2019-10-10) Next changeset 6:d46d803ca6cc (2021-01-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715"

modified:
macros.xml
maker.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

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

removed:
test-data/annot_repbase.gff3

diff -r 5e96efe6e6c6 -r 5201ec38c01f macros.xml
--- a/macros.xml Thu Oct 10 02:56:46 2019 -0400
+++ b/macros.xml Mon Dec 28 23:19:04 2020 +0000

@@ -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>

diff -r 5e96efe6e6c6 -r 5201ec38c01f maker.xml
--- a/maker.xml Thu Oct 10 02:56:46 2019 -0400
+++ b/maker.xml Mon Dec 28 23:19:04 2020 +0000

[

b'@@ -1,19 +1,23 @@\n <?xml version="1.0"?>\n-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1">\n+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">\n <description>genome annotation pipeline</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <command><![CDATA[\n- RM_LIB_PATH=\\$(dirname \\$(which RepeatMasker))/../share/RepeatMasker/Libraries &&\n- mkdir lib &&\n- export REPEATMASKER_LIB_DIR=\\$(pwd)/lib &&\n- for file in \\$(ls \\$RM_LIB_PATH) ; do ln -s \\$RM_LIB_PATH/\\$file lib/\\$file ; done &&\n- #if $repeat_masking.repeat_source.source_type == "repbase":\n- cp \'${repeat_masking.repeat_source.repbase_file}\' \'lib/${repeat_masking.repeat_source.repbase_file_name}\' &&\n+ RM_PATH=\\$(which RepeatMasker) &&\n+ if [ -z "\\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\\$PATH)" >&2 ; exit 1 ; fi &&\n+\n+ LIBDIR=\\$(dirname "\\$RM_PATH")/../share/RepeatMasker/Libraries &&\n+ #if $repeat_masking.repeat_source.source_type == "dfam_up":\n+ mkdir lib/ &&\n+ ln -s \'${repeat_masking.repeat_source.dfam_lib}\' lib/RepeatMaskerLib.h5 &&\n+ LIBDIR=\\$(pwd)/lib &&\n #end if\n \n+ export LIBDIR &&\n+\n maker -CTL\n \n &&\n@@ -35,7 +39,12 @@\n export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n #end if\n \n- mpiexec -n \\${GALAXY_SLOTS:-4} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null\n+ MPI_CMD="mpiexec -n \\${GALAXY_SLOTS:-4}" &&\n+ if [ "\\$MAKER_NO_MPI" != "1" ]; then\n+ MPI_CMD="";\n+ fi &&\n+\n+ \\${MPI_CMD} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null\n \n &&\n \n@@ -112,7 +121,7 @@\n #end if\n \n #-----Repeat Masking (leave values blank to skip repeat masking)\n-#if $repeat_masking.repeat_source.source_type == \'repbase\'\n+#if $repeat_masking.repeat_source.source_type == \'dfam\'\n \n #if $repeat_masking.repeat_source.species_source.species_from_list == \'yes\'\n model_org=${repeat_masking.repeat_source.species_source.species_list}\n@@ -123,6 +132,11 @@\n rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker\n softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n \n+#else if $repeat_masking.repeat_source.source_type == \'dfam_up\'\n+model_org=${repeat_masking.repeat_source.species_name}\n+rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker\n+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n+\n #else if $repeat_masking.repeat_source.source_type == \'library\'\n model_org= # select a model organism for RepBase masking in RepeatMasker\n #if $repeat_masking.repeat_source.rmlib\n@@ -385,14 +399,13 @@\n \n <section name="repeat_masking" title="Repeat masking" expanded="True">\n <conditional name="repeat_source">\n- <param label="Repeat library source" name="source_type" type="select">\n- <option selected="true" value="repbase">RepBase</option>\n+ <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose \'Custom library of repeats\' and select a fasta version of this non-free database.">\n+ <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option>\n+ <option value="dfam_up">DFam (full/specific version)</option>\n <option value="library">Custom library of repeats</option>\n <option value="no">Disable repeat masking (not recommended)</option>\n </param>\n- <when value="repbase">\n- <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />\n- '..b' to select repeats from DFam" />\n </when>\n </conditional>\n <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>\n </when>\n+ <when value="dfam_up">\n+ <param name="dfam_lib" type="data" format="h5" label="DFam library" help="The full DFam library can be downloaded from https://www.dfam.org/releases/current/families/Dfam.h5.gz" />\n+ <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />\n+ <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>\n+ </when>\n <when value="library">\n <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" />\n <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />\n@@ -548,13 +548,21 @@\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n- <param name="repeat_masking|repeat_source|source_type" value="repbase"/>\n- <param name="repeat_masking|repeat_source|repbase_file" value="fake_repbase.embl" />\n- <param name="repeat_masking|repeat_source|repbase_file_name" value="fake.embl" />\n- <param name="repeat_masking|repeat_source|species_list" value="anopheles" />\n- <output name="output_gff" file="annot_repbase.gff3"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="dfam"/>\n+ <param name="repeat_masking|repeat_source|species_list" value="drosophila" />\n+ <output name="output_gff" file="annot_dfam.gff3"/>\n <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>\n </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="est_evidences|est" value="est.fasta"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="dfam_up"/>\n+ <param name="repeat_masking|repeat_source|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />\n+ <param name="repeat_masking|repeat_source|species_name" value="rodent" />\n+ <output name="output_gff" file="annot_dfam_up.gff3"/>\n+ <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n 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.\n'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/Dfam_partial_test.h5

Binary file test-data/Dfam_partial_test.h5 has changed

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/annot_dfam.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_dfam.gff3 Mon Dec 28 23:19:04 2020 +0000

@@ -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
+###
+###

diff -r 5e96efe6e6c6 -r 5201ec38c01f 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 23:19:04 2020 +0000

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/annot_human.gff3
--- a/test-data/annot_human.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/annot_human.gff3 Mon Dec 28 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/annot_model.gff3
--- a/test-data/annot_model.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/annot_model.gff3 Mon Dec 28 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/annot_repbase.gff3
--- a/test-data/annot_repbase.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -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
-###
-###

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/evidences_human.gff3
--- a/test-data/evidences_human.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/evidences_human.gff3 Mon Dec 28 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/evidences_model.gff3
--- a/test-data/evidences_model.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/evidences_model.gff3 Mon Dec 28 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/evidences_norm.gff3
--- a/test-data/evidences_norm.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/evidences_norm.gff3 Mon Dec 28 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f 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 23:19:04 2020 +0000

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'

diff -r 5e96efe6e6c6 -r 5201ec38c01f test-data/evidences_reuse.gff3
--- a/test-data/evidences_reuse.gff3 Thu Oct 10 02:56:46 2019 -0400
+++ b/test-data/evidences_reuse.gff3 Mon Dec 28 23:19:04 2020 +0000

@@ -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