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Changeset 0:16e44ec438c4 (2017-10-19)

Next changeset 1:73a79dec987b (2018-07-01)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e

added:
macros.xml
maker.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

diff -r 000000000000 -r 16e44ec438c4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Oct 19 15:58:39 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>

diff -r 000000000000 -r 16e44ec438c4 maker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/maker.xml Thu Oct 19 15:58:39 2017 -0400

[

b'@@ -0,0 +1,486 @@\n+<?xml version="1.0"?>\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+ maker -CTL\n+\n+ &&\n+\n+ sed "s/cpus=/cpus=\\${GALAXY_SLOTS:-4}/g" \'$ctl\' > maker_opts.ctl\n+\n+ &&\n+\n+ #if $abinitio_gene_prediction.aug_prediction.augustus_mode == \'history\'\n+\n+ ## Using an augustus model from history, we need to unzip it and let augustus find it\n+\n+ cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n+\n+ mkdir -p \'augustus_dir/species/\' &&\n+\n+ tar -C \'augustus_dir/species/\' -xzvf \'${abinitio_gene_prediction.aug_prediction.augustus_model}\' > /dev/null &&\n+\n+ export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n+ #end if\n+\n+ maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl\n+\n+ &&\n+\n+ gff3_merge -d *.maker.output/*_master_datastore_index.log -o \'${output_full}\'\n+\n+ &&\n+\n+ awk \'{if ($2 == "maker" || $1 ~ /^\\#/) {print}}\' \'${output_full}\' | sed -n \'/^\\#\\#FASTA\\$/q;p\' > \'${output_gff}\'\n+\n+ &&\n+\n+ awk \'{if ($2 != "maker") {print}}\' \'${output_full}\' | sed -n \'/^\\#\\#FASTA\\$/q;p\' > \'${output_evidences}\'\n+ ]]></command>\n+ <configfiles>\n+ \n+ <configfile name="ctl"><![CDATA[\n+#-----Genome (these are always required)\n+genome=${genome} # genome sequence (fasta file or fasta embeded in GFF3 file)\n+organism_type=${organism_type} # eukaryotic or prokaryotic. Default is eukaryotic\n+\n+#-----Re-annotation Using MAKER Derived GFF3\n+#if $reannotation.reannotate == \'no\'\n+maker_gff= # MAKER derived GFF3 file\n+est_pass=0 # use ESTs in maker_gff: 1 = yes, 0 = no\n+altest_pass=0 # use alternate organism ESTs in maker_gff: 1 = yes, 0 = no\n+protein_pass=0 # use protein alignments in maker_gff: 1 = yes, 0 = no\n+rm_pass=0 # use repeats in maker_gff: 1 = yes, 0 = no\n+model_pass=0 # use gene models in maker_gff: 1 = yes, 0 = no\n+pred_pass=0 # use ab-initio predictions in maker_gff: 1 = yes, 0 = no\n+other_pass=0 # passthrough anything else in maker_gff: 1 = yes, 0 = no\n+#else\n+maker_gff=${reannotation.maker_gff} # MAKER derived GFF3 file\n+est_pass=${reannotation.est_pass} # use ESTs in maker_gff: 1 = yes, 0 = no\n+altest_pass=${reannotation.altest_pass} # use alternate organism ESTs in maker_gff: 1 = yes, 0 = no\n+protein_pass=${reannotation.protein_pass} # use protein alignments in maker_gff: 1 = yes, 0 = no\n+rm_pass=${reannotation.rm_pass} # use repeats in maker_gff: 1 = yes, 0 = no\n+model_pass=${reannotation.model_pass} # use gene models in maker_gff: 1 = yes, 0 = no\n+pred_pass=${reannotation.pred_pass} # use ab-initio predictions in maker_gff: 1 = yes, 0 = no\n+other_pass=${reannotation.other_pass} # passthrough anything else in maker_gff: 1 = yes, 0 = no\n+#end if\n+\n+#-----EST Evidence (for best results provide a file for at least one)\n+#if $est_evidences.est\n+est=${est_evidences.est} # set of ESTs or assembled mRNA-seq in fasta format\n+#else\n+est= # set of ESTs or assembled mRNA-seq in fasta format\n+#end if\n+#if $est_evidences.altest\n+altest=${est_evidences.altest} # EST/cDNA sequence file in fasta format from an alternate organism\n+#else\n+altest= # EST/cDNA sequence file in fasta format from an alternate organism\n+#end if\n+#if $est_evidences.est_gff\n+est_gff=${est_evidences.est_gff} # aligned ESTs or mRNA-seq from an external GFF3 file\n+#else\n+est_gff= # aligned ESTs or mRNA-seq from an external GFF3 file\n+#end if\n+#if $est_evidences.altest_gff\n+altest_gff=${est_evidences.altest_gff} # aligned ESTs from a closly relate species in GFF3 format\n+#else\n+altest_gff= # aligned ESTs from a closly relate species in GFF3 format\n+#end if\n+\n+#-----Protein Homology Evidence (for best results provide a file for at least one)\n+#if $protein_evidence'..b'e="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="organism_type" value="prokaryotic"/>\n+ <param name="est_evidences|est" value="est.fasta"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <output name="output_gff" file="annot_proc.gff3"/>\n+ <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="reannotation|reannotate" value="yes"/>\n+ <param name="reannotation|maker_gff" value="evidences.gff3"/>\n+ <param name="reannotation|est_pass" value="true"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <output name="output_gff" file="annot_reuse.gff3"/>\n+ <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>\n+ <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>\n+ <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>\n+ <param name="est_evidences|est" value="est.fasta"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>\n+ <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>\n+ <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>\n+ <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>\n+ <param name="est_evidences|est" value="est.fasta"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>\n+ <output name="output_evidences" file="evidences_model.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|repeatmasker|do_rm" value="no"/>\n+ <output name="output_gff" file="annot_norm.gff3"/>\n+ <output name="output_evidences" file="evidences_norm.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+\n+ .. _Maker: http://www.yandell-lab.org/software/maker.html\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 16e44ec438c4 test-data/annot.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3 Thu Oct 19 15:58:39 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
+###
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_human.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_human.gff3 Thu Oct 19 15:58:39 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
+###
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_mapped.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_mapped.gff3 Thu Oct 19 15:58:39 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;
+###
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_model.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_model.gff3 Thu Oct 19 15:58:39 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
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_norm.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_norm.gff3 Thu Oct 19 15:58:39 2017 -0400

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_proc.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_proc.gff3 Thu Oct 19 15:58:39 2017 -0400

@@ -0,0 +1,3 @@
+##gff-version 3
+###
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/annot_reuse.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_reuse.gff3 Thu Oct 19 15:58:39 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
+###
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/est.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est.fasta Thu Oct 19 15:58:39 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

diff -r 000000000000 -r 16e44ec438c4 test-data/evidences.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences.gff3 Thu Oct 19 15:58:39 2017 -0400

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\t9419\t9435\t16\t+\t.\tID=HS04636:hit:0:1.3.0.0;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:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +\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\t6918\t6977\t17\t+\t.\tID=HS04636:hit:3:1.3.0.0;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:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +\n+HS04636\t'..b'part\t6028\t6072\t21\t+\t.\tID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +\n+HS04636\trepeatmasker\tmatch\t4518\t4541\t17\t+\t.\tID=HS04636:hit:5:1.3.0.0;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:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +\n+HS04636\trepeatmasker\tmatch\t3852\t3888\t12\t+\t.\tID=HS04636:hit:6:1.3.0.0;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:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +\n+HS04636\trepeatmasker\tmatch\t3840\t3847\t17\t+\t.\tID=HS04636:hit:7:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +\n+HS04636\trepeatmasker\tmatch_part\t3840\t3847\t17\t+\t.\tID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +\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 000000000000 -r 16e44ec438c4 test-data/evidences_human.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_human.gff3 Thu Oct 19 15:58:39 2017 -0400

b'@@ -0,0 +1,99 @@\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+###\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:47:1.3.0.0;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:48:3.2.0.0;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:49:3.2.0.0;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:50:3.2.0.0;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:51:3.2.0.0;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:52:3.2.0.0;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:53:3.2.0.0;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:54:3.2.0.0;Parent=HS08198:hit:13:3.2.0'..b'epeatmasker\tmatch_part\t6028\t6072\t21\t+\t.\tID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +\n+HS04636\trepeatmasker\tmatch\t6918\t6977\t17\t+\t.\tID=HS04636:hit:5:1.3.0.0;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:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +\n+HS04636\trepeatmasker\tmatch\t3840\t3847\t17\t+\t.\tID=HS04636:hit:6:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +\n+HS04636\trepeatmasker\tmatch_part\t3840\t3847\t17\t+\t.\tID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +\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 000000000000 -r 16e44ec438c4 test-data/evidences_model.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_model.gff3 Thu Oct 19 15:58:39 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

diff -r 000000000000 -r 16e44ec438c4 test-data/evidences_norm.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_norm.gff3 Thu Oct 19 15:58:39 2017 -0400

diff -r 000000000000 -r 16e44ec438c4 test-data/evidences_proc.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_proc.gff3 Thu Oct 19 15:58:39 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
+###

diff -r 000000000000 -r 16e44ec438c4 test-data/evidences_reuse.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_reuse.gff3 Thu Oct 19 15:58:39 2017 -0400

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:11:3.12.0.0;Name=HS08198.g2;score=140\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n+HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n+HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n+HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869\n+HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46\n+HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162\n+HS08198\test2genome\tmatch_part\t812\t894\t2869\t+\t.\tID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n+HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n+HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n+HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS04636\t.\tcontig\t1\t9453\t.\t.\t.\tID=HS04636;Name=HS04636\n+###\n+HS04636\trepeatmasker\tmatch\t3852\t3888\t12\t+\t.\tID=HS04636:hit:0:1.3.0.0;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:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +\n+HS04636\trepeatmasker\tmatch\t6028\t6072\t21\t+\t.\tID=HS04636:hit:1:1.3.0.0;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:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +\n+HS04636\trepeatmasker\tmatch\t3840\t3847\t17\t+\t.\tID=HS04636:hit:2:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +\n+HS04636\trepeatmasker\tmatch_part\t3840\t3847\t17\t+\t.\tID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +\n+HS04636\trepeatmasker\tmatch\t3791\t3839\t22\t+\t.\tID=HS04636:hit:3:1.3.0.0;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:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528AC%2529n|genus:Simp'..b'arent=HS04636:hit:4:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +\n+HS04636\trepeatmasker\tmatch\t939\t980\t13\t+\t.\tID=HS04636:hit:5:1.3.0.0;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:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +\n+HS04636\trepeatmasker\tmatch\t6918\t6977\t17\t+\t.\tID=HS04636:hit:6:1.3.0.0;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:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +\n+HS04636\trepeatmasker\tmatch\t4518\t4541\t17\t+\t.\tID=HS04636:hit:7:1.3.0.0;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:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +\n+###\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:8:3.12.0.0;Name=HS04636.g1;score=120\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4541\t4790\t250\t+\t.\tID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t6008\t150\t+\t.\tID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:9:3.12.0.0;Name=HS04636.g1;score=8728\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:19:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:20:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:21:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:22:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:23:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:24:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:25:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:26:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n'

diff -r 000000000000 -r 16e44ec438c4 test-data/genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta Thu Oct 19 15:58:39 2017 -0400

b'@@ -0,0 +1,200 @@\n+>HS04636\n+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta\n+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt\n+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc\n+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag\n+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta\n+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac\n+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct\n+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc\n+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca\n+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga\n+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat\n+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg\n+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac\n+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca\n+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag\n+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg\n+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg\n+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc\n+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact\n+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca\n+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa\n+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata\n+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt\n+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg\n+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat\n+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta\n+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg\n+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt\n+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat\n+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg\n+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg\n+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga\n+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca\n+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct\n+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa\n+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc\n+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa\n+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac\n+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa\n+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta\n+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta\n+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg\n+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca\n+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca\n+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac\n+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag\n+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata\n+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca\n+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat\n+actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag\n+taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa\n+aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg\n+ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga\n+gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta\n+attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt\n+tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt\n+gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt\n+ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag\n+aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt\n+cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg\n+ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca\n+agggctaacattaaaggagatatacagatagatagatccaaataacttatccactttttt\n+taaaaagaagtcttatctataaaaaccttaaaggaattttccatttacttcactggtcta\n+gtaaaattatacacacacacagacatgcacacacatatataaacattcacacacatacat\n+at'..b'ccaagctgtgcttgaataacgatatgttttctcagattttc\n+tgttgtacagtttaatttagcagtccatatcacattgcaaaagtagcaatgacctcataa\n+aatacctcttcaaaatgcttaaattcatttcacacattaattttatctcagtcttgaagc\n+caattcagtaggtgcattggaatcaagcctggctacctgcatgctgttccttttcttttc\n+ttcttttagccattttgctaagagacacagtcttctcatcacttcgtttctcctattttg\n+ttttactagttttaagatcagagttcactttctttggactctgcctatattttcttacct\n+gaacttttgcaagttttcaggtaaacctcagctcaggactgctatttagctcctcttaag\n+aagattaaaagagaaaaaaaaaggcccttttaaaaatagtatacacttattttaagtgaa\n+aagcagagaattttatttatagctaattttagctatctgtaaccaagatggatgcaaaga\n+ggctagtgcctcagagagaactgtacggggtttgtgactggaaaaagttacgttcccatt\n+ctaattaatgccctttcttatttaaaaacaaaaccaaatgatatctaagtagttctcagc\n+aataataataatgacgataatacttcttttccacatctcattgtcactgacatttaatgg\n+tactgtatattacttaatttattgaagattattatttatgtcttattaggacactatggt\n+tataaactgtgtttaagcctacaatcattgatttttttttgttatgtcacaatcagtata\n+ttttctttggggttacctctctgaatattatgtaaacaatccaaagaaatgattgtatta\n+agatttgtgaataaatttttagaaatctgattggcatattgagatatttaaggttgaatg\n+tttgtccttaggataggcctatgtgctagcccacaaagaatattgtctcattagcctgaa\n+tgtgccataagactgaccttttaaaatgttttgagggatctgtggatgcttcgttaattt\n+gttcagccacaatttattgagaaaatattctgtgtcaagcactgtgggttttaatatttt\n+taaatcaaacgctgattacagataatagtatttatataaataattgaaaaaaattttctt\n+ttgggaagagggagaaaatgaaataaatatcattaaagataactcaggagaatcttcttt\n+acaattttacgtttagaatgtttaaggttaagaaagaaatagtcaatatgcttgtataaa\n+acactgttcactgttttttttaaaaaaaaaacttgatttgttattaacattgatctgctg\n+acaaaacctgggaatttgggttgtgtatgcgaatgtttcagtgcctcagacaaatgtgta\n+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa\n+aaaaaaaaaaaaaaatcgatgtcgactcgagtc\n+>HS08198\n+agcgggcggcggtcgtgggcggggttgcaggcgaggctcaacgaacgctggtctgaccgt\n+cggcgctccctgttgccgggccctgagcaagtggcttcatgaaccccgtgacgttggcca\n+tggagataagaccactgggtgatggtttaaggaagataacgtgtaaagggctaaggactg\n+tcggtggaaatcaggggtgcaggagaaatggataaacagccagaggtcaactcggacttt\n+gtacataggacatggtgccaggccctgccaggaagtgcagatcgaagctaggctcacgag\n+gaggctggaggtggggggtggggaggcaacggatggacatggacttcctgggctgggctc\n+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag\n+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg\n+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc\n+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt\n+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg\n+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc\n+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt\n+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac\n+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt\n+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg\n+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc\n+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag\n+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca\n+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc\n+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag\n+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg\n+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc\n+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta\n+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc\n+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga\n+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag\n+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc\n+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat\n+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac\n+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc\n+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc\n+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc\n+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg\n+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc\n+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc\n+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc\n+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc\n+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca\n+gccc\n'

diff -r 000000000000 -r 16e44ec438c4 test-data/id_map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/id_map.tsv Thu Oct 19 15:58:39 2017 -0400

@@ -0,0 +1,4 @@
+maker-HS04636-exonerate_est2genome-gene-0.0 YES000001
+maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 YES000001-RA
+maker-HS08198-exonerate_est2genome-gene-0.0 YES000002
+maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 YES000002-RA

diff -r 000000000000 -r 16e44ec438c4 test-data/local.tar.gz

Binary file test-data/local.tar.gz has changed

diff -r 000000000000 -r 16e44ec438c4 test-data/snap.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snap.hmm Thu Oct 19 15:58:39 2017 -0400

b'@@ -0,0 +1,1612 @@\n+zoeHMM snap_training 6 8 6 7\n+\n+<STATES>\n+\n+Einit\t0\t0\t3\t-1\texplicit\n+Esngl\t0\t0\t150\t-1\texplicit\n+Eterm\t0\t0\t3\t-1\texplicit\n+Exon\t0\t0\t6\t-1\texplicit\n+Inter\t0.9\t0.9\t0\t0\tgeometric\n+Intron\t0.1\t0.1\t0\t0\tgeometric\n+\n+<STATE_TRANSITIONS>\n+\n+Einit\tIntron\t1\n+Esngl\tInter\t1\n+Eterm\tInter\t1\n+Exon\tIntron\t1\n+Inter\tEinit\t1.000000\n+Inter\tEsngl\t0.000000\n+Intron\tEterm\t0.153846\n+Intron\tExon\t0.846154\n+\n+<PHASE_PREFERENCES>\n+\n+0.500000\n+0.500000\n+0.000000\n+0.333333\n+0.666667\n+0.000000\n+0.571429\n+0.428571\n+0.000000\n+0.000000\n+1.000000\n+0.000000\n+1.000000\n+0.000000\n+0.750000\n+0.250000\n+1.000000\n+0.000000\n+\n+<STATE_DURATIONS>\n+\n+Einit 2\n+\tDEFINED 0 249\n+\t\t-2.459 -2.611 -2.781 -2.974 -3.196 \n+\t\t-3.459 -3.781 -4.196 -4.781 -5.781 \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\t\t. . . . . \n+\tGEOMETRIC 250 -1\n+\t\t3\n+\n+Esngl 1\n+\tGEOMETRIC 0 -1\n+\t\t1000\n+\n+Eterm 2\n+\tDEFINED 0 249\n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -10.052 -9.080 -8.505 -8.095 \n+\t\t-7.776 -7.515 -7.294 -7.102 -6.933 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.782 -6.782 -6.782 -6.782 \n+\t\t-6.782 -6.933 -7.102 -7.294 -7.515 \n+\t\t-7.776 -8.095 -8.505 -9.080 -10.052 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\t\t-14.718 -14.718 -14.718 -14.718 -14.718 \n+\tGEOMETRIC 250 -1\n+\t\t668\n+\n+Exon 2\n+\tDEFINED 0 249\n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777 \n+\t\t-16.777 -16.777 -16.777 -16.777 -16.777'..b'\t\n+\t-1.087\t0.720\t-2.087\t0.720\t\n+\t-0.632\t0.046\t0.368\t0.046\t\n+\t0.497\t-0.503\t0.234\t-0.503\t\n+\t0.348\t-2.459\t0.541\t0.126\t\n+\t0.300\t-0.115\t-1.700\t0.621\t\n+\t0.559\t0.074\t-0.663\t-0.248\t\n+\t-0.807\t-0.807\t0.515\t0.515\t\n+\t0.652\t-1.807\t0.778\t-1.222\t\n+\t0.263\t0.678\t-1.322\t-0.322\t\n+\t0.752\t0.074\t-1.248\t-0.248\t\n+\t0.585\t-1.000\t-0.585\t0.415\t\n+\t0.000\t0.000\t0.415\t-0.585\t\n+\t-0.222\t1.000\t-1.807\t-0.222\t\n+\t-0.322\t0.678\t-0.322\t-0.322\t\n+\t0.126\t-0.459\t-0.459\t0.541\t\n+\t-0.322\t-0.737\t1.000\t-0.737\t\n+\t0.193\t0.778\t-1.807\t-0.222\t\n+\t-0.939\t0.284\t0.798\t-0.939\t\n+\t-0.322\t0.415\t-0.322\t0.093\t\n+\t-0.737\t-1.322\t0.000\t1.000\t\n+\t-0.459\t0.541\t-1.459\t0.541\t\n+\t-0.807\t-0.392\t-0.392\t0.930\t\n+\t-0.402\t-0.888\t0.376\t0.491\t\n+\t0.925\t-0.561\t-0.713\t-0.298\t\n+\t0.000\t-0.415\t-2.000\t1.000\t\n+\t0.759\t0.300\t-1.115\t-0.700\t\n+\t-0.170\t-0.755\t-0.170\t0.705\t\n+\t-0.070\t-1.392\t0.608\t0.193\t\n+\t0.234\t-0.503\t-1.087\t0.720\t\n+\t-0.585\t-0.585\t1.000\t-0.585\t\n+\t-0.503\t-1.087\t0.497\t0.497\t\n+\t0.052\t-0.433\t0.052\t0.245\t\n+\t0.752\t-0.663\t-2.248\t0.559\t\n+\t0.415\t0.415\t-1.585\t0.000\t\n+\t-0.115\t-0.115\t0.107\t0.107\t\n+\t0.663\t-0.415\t-1.263\t0.322\t\n+\t0.234\t-1.087\t-2.087\t1.082\t\n+\t0.193\t-0.070\t-1.392\t0.608\t\n+\t-0.143\t-2.143\t-0.558\t1.130\t\n+\t0.678\t-0.644\t-0.059\t-0.322\t\n+\t0.585\t0.000\t-1.000\t0.000\t\n+\t-0.737\t0.263\t-0.322\t0.485\t\n+\t0.152\t-0.170\t-0.585\t0.415\t\n+\t-0.737\t0.263\t0.263\t0.000\t\n+\t0.930\t-0.070\t-1.392\t-0.392\t\n+\t-1.170\t1.152\t-1.170\t-0.170\t\n+\t-1.644\t-0.322\t0.678\t0.356\t\n+\t-0.585\t-0.585\t1.000\t-0.585\t\n+\t0.193\t0.778\t-0.807\t-0.807\t\n+\t-0.585\t1.000\t-0.585\t-0.585\t\n+\t0.193\t0.193\t-0.807\t0.193\t\n+\t0.608\t-1.392\t-0.070\t0.193\t\n+\t0.263\t0.678\t-1.322\t-0.322\t\n+\t-0.585\t0.637\t-0.585\t0.152\t\n+\t0.415\t-0.237\t-0.237\t-0.044\t\n+\t0.759\t-1.700\t-0.115\t0.107\t\n+\t0.678\t0.485\t-1.322\t-0.737\t\n+\t-1.322\t0.263\t-0.322\t0.678\t\n+\t0.126\t0.126\t-0.459\t0.126\t\n+\t0.000\t-0.322\t0.678\t-0.737\t\n+\t0.222\t0.000\t-0.585\t0.222\t\n+\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t0.193\t-0.222\t-0.222\t0.193\t\n+\t-1.170\t-1.170\t0.152\t1.000\t\n+\t-1.248\t0.074\t-0.663\t0.922\t\n+\t-0.059\t-0.644\t0.526\t-0.059\t\n+\t-0.524\t0.061\t0.061\t0.284\t\n+\t0.263\t-0.585\t-0.322\t0.415\t\n+\t-0.503\t0.497\t-2.087\t0.720\t\n+\t-0.379\t-0.700\t1.107\t-1.115\t\n+\t-0.193\t-1.000\t-0.678\t1.000\t\n+\t1.037\t-0.700\t-0.963\t-0.285\t\n+\t0.152\t0.152\t-2.170\t0.637\t\n+\t0.245\t-0.170\t-1.170\t0.567\t\n+\t0.255\t-1.248\t-1.248\t0.974\t\n+\t0.515\t-0.222\t0.000\t-0.485\t\n+\t0.798\t-0.939\t-1.524\t0.476\t\n+\t-0.170\t-1.170\t-0.170\t0.830\t\n+\t0.126\t-0.044\t-1.459\t0.656\t\n+\t0.816\t0.163\t-1.059\t-0.644\t\n+\t0.000\t0.585\t-1.000\t0.000\t\n+\t0.263\t-0.737\t-0.737\t0.678\t\n+\t0.227\t-1.358\t-0.188\t0.642\t\n+\t-0.026\t-0.663\t-0.373\t0.691\t\n+\t0.491\t-0.209\t-2.209\t0.598\t\n+\t-0.115\t-1.285\t-0.115\t0.802\t\n+\t0.258\t-1.015\t-0.899\t0.826\t\n+\n+Start SDT 3 0 4 2 0.000\n+\tATG WMM 15 9 4 0 0.000\n+\t\t-0.585\t-0.585\t1.000\t-0.585\t\n+\t\t-0.585\t0.415\t0.415\t-0.585\t\n+\t\t-0.585\t0.415\t-0.585\t0.415\t\n+\t\t-0.585\t-0.585\t1.000\t-0.585\t\n+\t\t-0.585\t0.415\t-0.585\t0.415\t\n+\t\t0.415\t0.415\t-0.585\t-0.585\t\n+\t\t0.415\t-0.585\t-0.585\t0.415\t\n+\t\t-0.585\t0.415\t0.415\t-0.585\t\n+\t\t-0.585\t0.415\t-0.585\t0.415\t\n+\t\t1.000\t-0.585\t-0.585\t-0.585\t\n+\t\t-0.585\t-0.585\t-0.585\t1.000\t\n+\t\t-0.585\t-0.585\t1.000\t-0.585\t\n+\t\t0.415\t0.415\t-0.585\t-0.585\t\n+\t\t-0.585\t-0.585\t0.415\t0.415\t\n+\t\t-0.585\t-0.585\t0.415\t0.415\t\n+\tNNN TRM 0 0 0 0 0.000\n+\n+Stop SDT 3 0 4 4 0.000\n+\tTAA WMM 9 6 4 0 0.000\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\t\t0.000\t0.000\t0.000\t0.000\t\n+\tTAG WMM 9 6 4 0 0.000\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t0.678\t-0.322\t-0.322\t-0.322\t\n+\t\t0.678\t-0.322\t-0.322\t-0.322\t\n+\t\t-0.322\t0.678\t-0.322\t-0.322\t\n+\t\t-0.322\t-0.322\t-0.322\t0.678\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t-0.322\t-0.322\t-0.322\t0.678\t\n+\t\t0.678\t-0.322\t-0.322\t-0.322\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\tTGA WMM 9 6 4 0 0.000\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t-0.322\t0.678\t-0.322\t-0.322\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t-0.322\t-0.322\t-0.322\t0.678\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t-0.322\t-0.322\t-0.322\t0.678\t\n+\t\t-0.322\t-0.322\t0.678\t-0.322\t\n+\t\t0.678\t-0.322\t-0.322\t-0.322\t\n+\tNNN TRM 0 0 0 0 0.000\n+\n'