changeset 0:c4ac24510b55 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
author iuc
date Sun, 03 Jan 2021 14:58:58 +0000
parents
children 1fdc517743e6
files locuspocus.xml macros.xml test-data/TAIR10_GFF3_alignment.gff test-data/TAIR10_GFF3_genes.gff test-data/TAIR9_GFF3_genes.gff test-data/canon-output_test1.gff3 test-data/canon-output_test2.gff3 test-data/canon-output_test3.gff3 test-data/gaeval_output_test1.txt test-data/gaeval_output_test2.txt test-data/gaeval_output_test3.txt test-data/locuspocus_genemap_test7.txt test-data/locuspocus_genemap_test8.txt test-data/locuspocus_lenght_test7.txt test-data/locuspocus_lenght_test8.txt test-data/locuspocus_output_test1.txt test-data/locuspocus_output_test2.txt test-data/locuspocus_output_test3.txt test-data/locuspocus_output_test4.txt test-data/locuspocus_output_test5.txt test-data/locuspocus_output_test6.txt test-data/locuspocus_output_test7.txt test-data/locuspocus_output_test8.txt test-data/locuspocus_transmap_test7.txt test-data/locuspocus_transmap_test8.txt test-data/parseval_output_test1.txt test-data/parseval_output_test2.txt test-data/parseval_output_test3.txt test-data/parseval_output_test4.html test-data/parseval_output_test5.html test-data/parseval_output_test6.txt
diffstat 31 files changed, 4105 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/locuspocus.xml	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,236 @@
+<tool id='aegean_locuspocus' name='AEGeAn LocusPocus' version='@TOOL_VERSION@' profile='20.01'>
+    <description> calculate locus coordinates for the given gene annotation</description>
+    <macros>                                                                                           
+        <import>macros.xml</import>
+    </macros>                                                                                          
+    <expand macro='xrefs'/>
+    <expand macro='edam_ontology'/>
+    <expand macro='requirements'/>
+    <version_command>locuspocus --version</version_command>
+    <command detect_errors='exit_code'>
+        <![CDATA[
+            locuspocus '$genesgff3'
+            -l $ilocus_parsing.delta
+            $ilocus_parsing.mode
+            $ilocus_parsing.skipiloci
+            #if $refine_options.refine_parameters.refine
+                $refine_options.refine_parameters.cds
+            #end if 
+            -m $refine_options.minoverlap
+            -f '$input_options.filter'
+            #if $input_options.parent
+                -p '$input_options.parent'
+            #end if
+            $input_options.pseudo
+            #if $output_options.outputfiles
+	            #if "ilens" in $output_options.outputfiles
+                    --ilens '$output_ilens'
+                #end if
+                #if "genemap" in $output_options.outputfiles
+                    --genemap '$output_genemap'
+                #end if
+                #if "transmap" in $output_options.outputfiles
+                    --transmap '$output_transmap'
+                #end if
+            #end if
+            #if $output_options.namefmt
+                -n '$output_options.namefmt'
+            #end if
+            $output_options.retainids
+            -o '$output'
+            ]]>
+    </command>
+    <inputs>
+        <param name='genesgff3' type='data' format='gff3' label="GFF3 File" />
+        <section name='ilocus_parsing' title='iLocus parsing options' expanded='True'>
+            <param argument='--delta' type='integer' 
+                min='0' max='1000' value='500'
+                label='Gene loci extension'
+                help='When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions' />
+            <param name='mode' type='select' label='Annotation mode'>
+                <option value='' selected='true'>Default mode</option>
+                <option value='--skipends'> Exclude unannotated iLoci at either end of the sequence</option>
+                <option value='--endsonly'> Report only incomplete iLocus fragments at the unannotated ends of sequences</option>
+            </param>
+            <param argument="--skipiloci"  type='boolean'            
+                truevalue='--skipiiloci' falsevalue=''
+                label='Do not report intergenic iLoci' />
+        </section>
+        <section name='refine_options' title='Refine options' expanded='false'>
+            <conditional name='refine_parameters'>
+                <param name='refine' type='select' 
+                    label='Mode for handling of overlpping genes'
+                    help='Refine mode allows for a more nuanced handling of overlapping genes.'>
+                    <option value=''>Default</option>
+                    <option value='--refine'>Refine mode</option>
+                </param>
+                <when value=''/>
+                <when value='--refine'>
+                    <param argument='--cds' type='boolean' 
+                        truevalue='--cds' falsevalue=''
+                        label='Use CDS rather than UTRs'
+                        help='(-c)' />
+                </when>
+            </conditional>
+            <param argument='--minoverlap' type='integer' 
+                max='20' min='1' value='1' 
+                label='Minimum number of overlapping nucleotides'
+                help='The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus' />
+        </section>
+        <section name='input_options' title='Input options' expanded='false'>
+            <param  argument='--filter' type='text' 
+                value='gene'
+                label='Comma-separated list of feature types to use'
+                help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)." />
+            <param argument='--parent' type='text' 
+                value='' optional='true'
+                label='Create a parent for features that lack a parent feature'
+                help='If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature  as a parent for any top-level mRNA feature.'/>
+            <param argument='--pseudo' type='boolean' 
+                truevalue='--pseudo' falsevalue=''
+                label='Correct erroneously labeled pseudogenes'/>   
+        </section>
+        <section name='output_options' title='Output options' expanded='false'>
+            <param argument='--retainids' type='boolean'
+                truevalue='--retainids' falsevalue=''
+                label='Retain original feature IDs'
+                help='Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values'/>
+            <param argument='--namefmt' type='text'
+                value='' optional='true'
+                label='ID format for newly created locy'
+                help='Provide a format string to override the default ID format for newly created loci; default is "locus%lu" (locus1, locus2, etc) for loci and "iLocus%lu" (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value.'/>
+            <param name="outputfiles" type="select" display="checkboxes" label="Output files"
+                multiple="true" optional="true" >
+                <option value="ilens">Create file with the lenghts of each intergenic iLocus</option>
+                <option value="genemap">Create a mapping from each gene annotation to its correspondig locus</option>
+                <option value="transmap">Create a mapping from each transcript annotation to its correspondent locus</option>
+            </param>
+        </section>
+
+    </inputs>
+    <outputs>
+        <data name='output' format='tabular' />
+        <data name='output_ilens' format='tabular'>
+            <filter>output_options['outputfiles'] and "ilens" in output_options['outputfiles']</filter>
+        </data>
+        <data name='output_genemap' format='tabular'>
+            <filter>output_options['outputfiles'] and "genemap" in output_options['outputfiles']</filter>
+        </data>
+        <data name='output_transmap' format='tabular'>
+            <filter>output_options['outputfiles'] and "transmap" in output_options['outputfiles']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <output name='output' file='locuspocus_output_test1.txt'/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='ilocus_parsing'>
+                <param name='delta' value='400'/>
+                <param name='mode' value='--skipends'/>
+            </section>
+            <output name='output' file='locuspocus_output_test2.txt'/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='ilocus_parsing'>
+                <param name='skipiloci' value='true'/>
+                <param name='mode' value='--endsonly'/>
+            </section>
+            <output name='output' file='locuspocus_output_test3.txt'/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='refine_options'>
+                <param name='refine_parameters|refine' value='--refine'/>
+                <param name='minoverlap' value='5'/>
+            </section>	    
+            <output name='output' file='locuspocus_output_test4.txt'/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='input_options'>
+                <param name='filter' value='gene,intron'/>
+                <param name='parent' value='mRNA:gene'/>
+            </section>	    
+            <output name='output' file='locuspocus_output_test5.txt'/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='input_options'>
+                <param name='filter' value='gene,intron'/>
+                <param name='parent' value='mRNA:gene'/>
+                <param name='pseudo' value='true'/>
+            </section>	    
+            <output name='output' file='locuspocus_output_test6.txt'/>
+        </test>
+        <test expect_num_outputs="4">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+            <section name='output_options'>
+                <param name='retainids' value='true'/>
+                <param name='namefmt' value='test%lu'/>
+                <param name='outputfiles' value='ilens,genemap,transmap'/>
+            </section>
+            <output name='output' file='locuspocus_output_test7.txt'/>
+            <output name='output_ilens' file='locuspocus_lenght_test7.txt'/>
+            <output name='output_genemap' file='locuspocus_genemap_test7.txt'/>
+            <output name='output_transmap' file='locuspocus_transmap_test7.txt'/>
+        </test>
+        <test expect_num_outputs="4">
+            <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/>
+	        <section name='refine_options'>
+                <param name='refine_parameters|refine' value='--refine'/>
+                <param name='refine_options|minoverlap' value='5'/>
+	        </section>
+            <section name='ilocus_parsing'>
+                <param name='delta' value='400'/>
+                <param name='mode' value='--skipends'/>
+            </section>
+            <section name='input_options'>
+                <param name='filter' value='gene,intron'/>
+                <param name='parent' value='mRNA:gene'/>
+            </section>	    
+            <section name='output_options'>
+                <param name='retainids' value='true'/>
+                <param name='outputfiles' value='ilens,genemap,transmap'/>
+            </section>
+            <output name='output' file='locuspocus_output_test8.txt'/>
+            <output name='output_ilens' file='locuspocus_lenght_test8.txt'/>
+            <output name='output_genemap' file='locuspocus_genemap_test8.txt'/>
+            <output name='output_transmap' file='locuspocus_transmap_test8.txt'/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+.. class:: infomark
+            
+**Purpose**
+            
+LocusPocus is a program for computing interval loci (iLoci) from a provided set gene annotations. Each iLocus corresponds to a single gene, a set of overlapping genes, or a space between genes. See this page for a description of iLoci as an organizational principle for genomics.
+            
+-----
+            
+.. class:: infomark
+            
+**Input**
+            
+Input for LocusPocus is one or more files in GFF3 format. The only strict requirement is that the input must be valid GFF3.
+            
+The use of ##sequence-region pragmas is optional, and many GFF3 files do not include them. LocusPocus uses this information when computing the location of iLoci at the ends of a sequence. Note that if these pragmas are not declared explicitly, iLoci will only be reported for sequence regions containing annotated features.
+            
+Users can override gene as the default feature of interest, replace it with one or more other feature types, and construct iLoci for these features in the same way.
+            
+-----
+            
+.. class:: infomark
+            
+**Output**
+            
+LocusPocus computes the location of the iLoci from the given gene features and reports the iLocus locations in GFF3 format. By default, only the iLocus features themselves are reported, with attributes indicating the number of genes and transcripts in the locus. 
+            
+]]>
+    </help>
+    <expand macro='citations'/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,36 @@
+<macros>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_3511</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0362</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+        <xref type='bio.tools'>gaeval</xref>
+      </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.16.0">aegean</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">                                                                   
+                @misc{githubAEGeAn,                                                                   
+                author = {Standage, Daniel S.},                                                    
+                year = {2015},                                                                 
+                title = {AEGeAn},                                                        
+                publisher = {GitHub},
+                journal = {GitHub repository},                                               
+                url = {https://github.com/BrendelGroup/AEGeAn},                        
+                }                                                                    
+            </citation>
+        </citations>
+    </xml>
+    <token name="@TOOL_VERSION@">0.16.0</token>
+
+</macros>   
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TAIR10_GFF3_alignment.gff	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,100 @@
+##gff-version 3
+##sequence-region   4 4174 18579887
+##sequence-region   Pt 11940 153877
+##sequence-region   3 9604 23458280
+##sequence-region   Mt 11727 332944
+##sequence-region   2 1089 19696461
+##sequence-region   1 3915 30423724
+##sequence-region   5 1227 26970443
+Pt	.	BED_feature	11940	12653	0	+	.	Name=region_0
+Pt	.	BED_feature	21863	22652	0	+	.	Name=region_1
+Pt	.	BED_feature	47925	48082	0	+	.	Name=region_2
+Pt	.	BED_feature	70139	70652	0	+	.	Name=region_3
+Pt	.	BED_feature	70946	71811	0	+	.	Name=region_4
+Pt	.	BED_feature	74848	75650	0	+	.	Name=region_5
+Pt	.	BED_feature	76490	77197	0	+	.	Name=region_6
+Pt	.	BED_feature	81589	82643	0	+	.	Name=region_7
+Pt	.	BED_feature	84773	85453	0	+	.	Name=region_8
+Pt	.	BED_feature	95704	96387	0	+	.	Name=region_9
+Pt	.	BED_feature	98026	98561	0	+	.	Name=region_10
+Pt	.	BED_feature	102404	136227	0	+	.	Name=region_11
+Pt	.	BED_feature	104306	105441	0	+	.	Name=region_12
+Pt	.	BED_feature	106980	131646	0	+	.	Name=region_13
+Pt	.	BED_feature	107004	131670	0	+	.	Name=region_14
+Pt	.	BED_feature	120378	121456	0	+	.	Name=region_15
+Pt	.	BED_feature	133209	134344	0	+	.	Name=region_16
+Pt	.	BED_feature	140089	140624	0	+	.	Name=region_17
+Pt	.	BED_feature	142263	142946	0	+	.	Name=region_18
+Pt	.	BED_feature	153197	153877	0	+	.	Name=region_19
+Mt	.	BED_feature	11727	188840	0	+	.	Name=region_20
+Mt	.	BED_feature	20719	21691	0	+	.	Name=region_21
+Mt	.	BED_feature	80134	81112	0	+	.	Name=region_22
+Mt	.	BED_feature	108929	108982	0	+	.	Name=region_23
+Mt	.	BED_feature	132215	133176	0	+	.	Name=region_24
+Mt	.	BED_feature	136074	137891	0	+	.	Name=region_25
+Mt	.	BED_feature	141941	142768	0	+	.	Name=region_26
+Mt	.	BED_feature	143479	146989	0	+	.	Name=region_27
+Mt	.	BED_feature	162155	163624	0	+	.	Name=region_28
+Mt	.	BED_feature	239003	260663	0	+	.	Name=region_29
+Mt	.	BED_feature	242068	260713	0	+	.	Name=region_30
+Mt	.	BED_feature	288110	289002	0	+	.	Name=region_31
+Mt	.	BED_feature	328080	329734	0	+	.	Name=region_32
+Mt	.	BED_feature	330308	332944	0	+	.	Name=region_33
+4	.	BED_feature	4174	4264	0	+	.	Name=region_34
+4	.	BED_feature	4440	4544	0	+	.	Name=region_35
+4	.	BED_feature	4751	4838	0	+	.	Name=region_36
+4	.	BED_feature	4903	4976	0	+	.	Name=region_37
+4	.	BED_feature	5121	5405	0	+	.	Name=region_38
+4	.	BED_feature	5590	5656	0	+	.	Name=region_39
+4	.	BED_feature	5857	6604	0	+	.	Name=region_40
+4	.	BED_feature	6678	6759	0	+	.	Name=region_41
+4	.	BED_feature	6873	6974	0	+	.	Name=region_42
+4	.	BED_feature	7058	7143	0	+	.	Name=region_43
+4	.	BED_feature	7196	7293	0	+	.	Name=region_44
+4	.	BED_feature	7640	7711	0	+	.	Name=region_45
+4	.	BED_feature	7836	8000	0	+	.	Name=region_46
+4	.	BED_feature	8157	8243	0	+	.	Name=region_47
+4	.	BED_feature	8370	8462	0	+	.	Name=region_48
+4	.	BED_feature	9439	9685	0	+	.	Name=region_49
+4	.	BED_feature	9849	9981	0	+	.	Name=region_50
+4	.	BED_feature	10127	10210	0	+	.	Name=region_51
+4	.	BED_feature	11794	11896	0	+	.	Name=region_52
+4	.	BED_feature	12018	12130	0	+	.	Name=region_53
+4	.	BED_feature	12181	12261	0	+	.	Name=region_54
+4	.	BED_feature	12442	12572	0	+	.	Name=region_55
+4	.	BED_feature	12708	12790	0	+	.	Name=region_56
+4	.	BED_feature	12811	12923	0	+	.	Name=region_57
+4	.	BED_feature	12961	13171	0	+	.	Name=region_58
+4	.	BED_feature	14030	14113	0	+	.	Name=region_59
+4	.	BED_feature	14181	14257	0	+	.	Name=region_60
+4	.	BED_feature	14835	14920	0	+	.	Name=region_61
+4	.	BED_feature	17956	18029	0	+	.	Name=region_62
+4	.	BED_feature	18515	18599	0	+	.	Name=region_63
+4	.	BED_feature	18694	18804	0	+	.	Name=region_64
+4	.	BED_feature	18872	19295	0	+	.	Name=region_65
+4	.	BED_feature	18872	19323	0	+	.	Name=region_66
+4	.	BED_feature	19675	19761	0	+	.	Name=region_67
+4	.	BED_feature	22299	22686	0	+	.	Name=region_68
+4	.	BED_feature	23201	23273	0	+	.	Name=region_69
+4	.	BED_feature	23386	23457	0	+	.	Name=region_70
+4	.	BED_feature	23386	23461	0	+	.	Name=region_71
+4	.	BED_feature	23386	23470	0	+	.	Name=region_72
+4	.	BED_feature	25220	25293	0	+	.	Name=region_73
+4	.	BED_feature	25412	25558	0	+	.	Name=region_74
+4	.	BED_feature	25681	25817	0	+	.	Name=region_75
+4	.	BED_feature	25743	25817	0	+	.	Name=region_76
+4	.	BED_feature	25882	26338	0	+	.	Name=region_77
+4	.	BED_feature	26412	26500	0	+	.	Name=region_78
+4	.	BED_feature	26754	26868	0	+	.	Name=region_79
+4	.	BED_feature	26754	26883	0	+	.	Name=region_80
+4	.	BED_feature	27005	27218	0	+	.	Name=region_81
+4	.	BED_feature	27005	27245	0	+	.	Name=region_82
+4	.	BED_feature	27010	27218	0	+	.	Name=region_83
+4	.	BED_feature	27280	27382	0	+	.	Name=region_84
+4	.	BED_feature	27425	27521	0	+	.	Name=region_85
+4	.	BED_feature	27601	27687	0	+	.	Name=region_86
+4	.	BED_feature	27774	27867	0	+	.	Name=region_87
+4	.	BED_feature	28021	28155	0	+	.	Name=region_88
+4	.	BED_feature	28078	28155	0	+	.	Name=region_89
+4	.	BED_feature	28283	28372	0	+	.	Name=region_90
+4	.	BED_feature	28283	28398	0	+	.	Name=region_91
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TAIR10_GFF3_genes.gff	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,100 @@
+Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
+Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
+Chr1	TAIR10	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1
+Chr1	TAIR10	protein	7315	8666	.	-	.	ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;Index=1
+Chr1	TAIR10	protein	11864	12940	.	-	.	ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1,AT1G01030.1-Protein;
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;Index=1
+Chr1	TAIR10	protein	23519	31079	.	+	.	ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TAIR9_GFF3_genes.gff	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,100 @@
+Chr1	TAIR9	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
+Chr1	TAIR9	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
+Chr1	TAIR9	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	Parent=AT1G01010.1,AT1G01010.1-Protein;
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
+Chr1	TAIR9	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	Parent=AT1G01020.1,AT1G01020.1-Protein;
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1
+Chr1	TAIR9	protein	7315	8666	.	-	.	ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	Parent=AT1G01020.2,AT1G01020.2-Protein;
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;Index=1
+Chr1	TAIR9	protein	11864	12940	.	-	.	ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1,AT1G01030.1-Protein;
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;Index=1
+Chr1	TAIR9	protein	23519	31079	.	+	.	ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	Parent=AT1G01040.1,AT1G01040.1-Protein;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/canon-output_test1.gff3	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,136 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS2;Parent=AT1G01020.2
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/canon-output_test2.gff3	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,136 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	test_source	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	test_source	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1
+Chr1	test_source	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	test_source	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	test_source	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+Chr1	test_source	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	test_source	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1
+Chr1	test_source	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	6915	7069	.	-	2	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	CDS	7157	7232	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	7384	7450	.	-	1	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	7564	7649	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	7762	7835	.	-	2	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	7942	7987	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	8236	8325	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	8417	8464	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	CDS	8571	8666	.	-	0	ID=CDS1;Parent=AT1G01020.1
+Chr1	test_source	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	test_source	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1
+Chr1	test_source	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	7070	7156	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	CDS	7315	7450	.	-	1	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	intron	7451	7563	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	7650	7761	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	7836	7941	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	7988	8235	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	8326	8416	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	intron	8465	8570	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	test_source	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.2
+Chr1	test_source	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	test_source	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+Chr1	test_source	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	test_source	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1
+Chr1	test_source	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	test_source	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	test_source	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+Chr1	test_source	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	test_source	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1
+Chr1	test_source	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	23519	24451	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	24542	24655	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	24752	24962	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	25041	25435	.	+	2	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	25524	25743	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	25825	25997	.	+	2	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	26081	26203	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	26292	26452	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	26543	26776	.	+	1	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	26862	27012	.	+	1	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	27099	27281	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	test_source	CDS	27372	27533	.	+	0	ID=CDS3;Parent=AT1G01040.1
+Chr1	test_source	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/canon-output_test3.gff3	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,136 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=gene1;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=mRNA1;Parent=gene1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=mRNA1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=mRNA1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=mRNA1
+Chr1	.	intron	3914	3995	.	+	.	Parent=mRNA1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=mRNA1
+Chr1	.	intron	4277	4485	.	+	.	Parent=mRNA1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=mRNA1
+Chr1	.	intron	4606	4705	.	+	.	Parent=mRNA1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=mRNA1
+Chr1	.	intron	5096	5173	.	+	.	Parent=mRNA1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=mRNA1
+Chr1	.	intron	5327	5438	.	+	.	Parent=mRNA1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=mRNA1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=mRNA1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=mRNA1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=mRNA1
+###
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=gene2;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=mRNA2;Parent=gene2;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=mRNA2
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=mRNA2
+Chr1	.	intron	6264	6436	.	-	.	Parent=mRNA2
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=mRNA2
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=mRNA2
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=mRNA2
+Chr1	.	intron	7233	7383	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=mRNA2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS2;Parent=mRNA2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=mRNA2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=mRNA2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=mRNA2
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=mRNA3;Parent=gene2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=mRNA3
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=mRNA3
+Chr1	.	intron	7070	7156	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=mRNA3
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=mRNA3
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=mRNA3
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS3;Parent=mRNA3
+Chr1	.	intron	7451	7563	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=mRNA3
+Chr1	.	intron	7650	7761	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=mRNA3
+Chr1	.	intron	7836	7941	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=mRNA3
+Chr1	.	intron	7988	8235	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=mRNA3
+Chr1	.	intron	8326	8416	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=mRNA3
+Chr1	.	intron	8465	8570	.	-	.	Parent=mRNA2,mRNA3
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS3;Parent=mRNA3
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=mRNA3
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=mRNA3
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=mRNA3
+###
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=gene3;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=mRNA4;Parent=gene3;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=mRNA4
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=mRNA4
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=mRNA4
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=mRNA4
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=mRNA4
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=mRNA4
+Chr1	.	intron	13174	13334	.	-	.	Parent=mRNA4
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=mRNA4
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=mRNA4
+###
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=gene4;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=mRNA5;Parent=gene4;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=mRNA5
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	24452	24541	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	24656	24751	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	24963	25040	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	25436	25523	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	25744	25824	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	25998	26080	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	26204	26291	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	26453	26542	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	26777	26861	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	27013	27098	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	intron	27282	27371	.	+	.	Parent=mRNA5
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=mRNA5
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS4;Parent=mRNA5
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=mRNA5
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gaeval_output_test1.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,143 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
+###
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.082
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+###
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7070	7156	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7451	7563	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7650	7761	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7836	7941	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7988	8235	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8326	8416	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8465	8570	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	protein	7315	8666	.	-	.	ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+###
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	protein	11864	12940	.	-	.	ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1,AT1G01030.1-Protein
+###
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	protein	23519	31079	.	+	.	ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gaeval_output_test2.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,143 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
+###
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.082
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+###
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7070	7156	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7451	7563	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7650	7761	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7836	7941	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7988	8235	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8326	8416	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8465	8570	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	protein	7315	8666	.	-	.	ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+###
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	protein	11864	12940	.	-	.	ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1,AT1G01030.1-Protein
+###
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	protein	23519	31079	.	+	.	ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gaeval_output_test3.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,143 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
+###
+Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.093
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	AEGeAn::GAEVAL	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein
+###
+Chr1	TAIR10	gene	5928	8737	.	-	.	ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.074
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.074
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7070	7156	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7451	7563	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7650	7761	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7836	7941	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	7988	8235	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8326	8416	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	intron	8465	8570	.	-	.	Parent=AT1G01020.1,AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	AEGeAn::GAEVAL	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein
+Chr1	TAIR10	protein	7315	8666	.	-	.	ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein
+###
+Chr1	TAIR10	gene	11649	13714	.	-	.	ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	AEGeAn::GAEVAL	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	protein	11864	12940	.	-	.	ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1,AT1G01030.1-Protein
+###
+Chr1	TAIR10	gene	23146	31227	.	+	.	ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	AEGeAn::GAEVAL	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	protein	23519	31079	.	+	.	ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_genemap_test7.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,4 @@
+AT1G01010	testXlu
+AT1G01020	testXlu
+AT1G01030	testXlu
+AT1G01040	testXlu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_genemap_test8.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,4 @@
+AT1G01010	locus:Chr1_3231-6299.
+AT1G01020	locus:Chr1_5528-9137.
+AT1G01030	locus:Chr1_11249-14114.
+AT1G01040	locus:Chr1_22746-31627.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_lenght_test7.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,3 @@
+Chr1	0
+Chr1	1911
+Chr1	8431
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_lenght_test8.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,3 @@
+Chr1	0
+Chr1	2111
+Chr1	8631
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test1.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	1	3130	.	.	.	.
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911
+Chr1	AEGeAn::LocusPocus	locus	9238	11148	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	liil=1911;child_gene=1;child_mRNA=1;riil=8431
+Chr1	AEGeAn::LocusPocus	locus	14215	22645	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	liil=8431;child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	31728	30427671	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test2.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,8 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	3231	6299	.	.	.	child_gene=1;child_mRNA=1;right_overlap=772;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5528	9137	.	.	.	left_overlap=772;liil=0;child_gene=1;child_mRNA=2;riil=2111
+Chr1	AEGeAn::LocusPocus	locus	9138	11248	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11249	14114	.	.	.	liil=2111;child_gene=1;child_mRNA=1;riil=8631
+Chr1	AEGeAn::LocusPocus	locus	14115	22745	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22746	31627	.	.	.	liil=8631;child_gene=1;child_mRNA=1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test3.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,6 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;child_gene=1;child_mRNA=2
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	child_gene=1;child_mRNA=1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test4.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	1	3130	.	.	.	.
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911
+Chr1	AEGeAn::LocusPocus	locus	9238	11148	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	liil=1911;child_gene=1;child_mRNA=1;riil=8431
+Chr1	AEGeAn::LocusPocus	locus	14215	22645	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	liil=8431;child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	31728	30427671	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test5.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	1	3130	.	.	.	.
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911
+Chr1	AEGeAn::LocusPocus	locus	9238	11148	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	liil=1911;child_gene=1;child_mRNA=1;riil=8431
+Chr1	AEGeAn::LocusPocus	locus	14215	22645	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	liil=8431;child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	31728	30427671	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test6.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	1	3130	.	.	.	.
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911
+Chr1	AEGeAn::LocusPocus	locus	9238	11148	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	liil=1911;child_gene=1;child_mRNA=1;riil=8431
+Chr1	AEGeAn::LocusPocus	locus	14215	22645	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	liil=8431;child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	31728	30427671	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test7.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,10 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	1	3130	.	.	.	Name=testXlu
+Chr1	AEGeAn::LocusPocus	locus	3131	6399	.	.	.	Name=testXlu;child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5428	9237	.	.	.	left_overlap=972;liil=0;Name=testXlu;child_gene=1;child_mRNA=2;riil=1911
+Chr1	AEGeAn::LocusPocus	locus	9238	11148	.	.	.	fg_orient=RR;Name=testXlu
+Chr1	AEGeAn::LocusPocus	locus	11149	14214	.	.	.	liil=1911;Name=testXlu;child_gene=1;child_mRNA=1;riil=8431
+Chr1	AEGeAn::LocusPocus	locus	14215	22645	.	.	.	fg_orient=RF;Name=testXlu
+Chr1	AEGeAn::LocusPocus	locus	22646	31727	.	.	.	liil=8431;Name=testXlu;child_gene=1;child_mRNA=1
+Chr1	AEGeAn::LocusPocus	locus	31728	30427671	.	.	.	Name=testXlu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_output_test8.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,8 @@
+##gff-version 3
+##sequence-region   Chr1 1 30427671
+Chr1	AEGeAn::LocusPocus	locus	3231	6299	.	.	.	child_gene=1;child_mRNA=1;right_overlap=772;iiLocus_exception=delta-overlap-gene;riil=0
+Chr1	AEGeAn::LocusPocus	locus	5528	9137	.	.	.	left_overlap=772;liil=0;child_gene=1;child_mRNA=2;riil=2111
+Chr1	AEGeAn::LocusPocus	locus	9138	11248	.	.	.	fg_orient=RR
+Chr1	AEGeAn::LocusPocus	locus	11249	14114	.	.	.	liil=2111;child_gene=1;child_mRNA=1;riil=8631
+Chr1	AEGeAn::LocusPocus	locus	14115	22745	.	.	.	fg_orient=RF
+Chr1	AEGeAn::LocusPocus	locus	22746	31627	.	.	.	liil=8631;child_gene=1;child_mRNA=1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_transmap_test7.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,5 @@
+AT1G01010.1	testXlu
+AT1G01020.1	testXlu
+AT1G01020.2	testXlu
+AT1G01030.1	testXlu
+AT1G01040.1	testXlu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locuspocus_transmap_test8.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,5 @@
+AT1G01010.1	locus:Chr1_3231-6299.
+AT1G01020.1	locus:Chr1_5528-9137.
+AT1G01020.2	locus:Chr1_5528-9137.
+AT1G01030.1	locus:Chr1_11249-14114.
+AT1G01040.1	locus:Chr1_22746-31627.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test1.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,577 @@
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=3626-5904
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01010
+|
+|  prediction genes:
+|    AT1G01010
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01010.1
+     |  prediction transcripts:
+     |    AT1G01010.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+ |
+     |  CDS structure comparison
+     |    6 reference  CDS segments
+     |    6 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    6 reference  exons
+     |    6 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    2 reference  UTR segments
+     |    2 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=5923-8742
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01020
+|
+|  prediction genes:
+|    AT1G01020
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.1
+     |  prediction transcripts:
+     |    AT1G01020.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+ |
+     |  CDS structure comparison
+     |    9 reference  CDS segments
+     |    9 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    10 reference  exons
+     |    10 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.2
+     |  prediction transcripts:
+     |    AT1G01020.2
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+ |
+     |  CDS structure comparison
+     |    7 reference  CDS segments
+     |    7 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    8 reference  exons
+     |    8 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=11644-13719
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01030
+|
+|  prediction genes:
+|    AT1G01030
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01030.1
+     |  prediction transcripts:
+     |    AT1G01030.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+ |
+     |  CDS structure comparison
+     |    1 reference  CDS segments
+     |    1 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    2 reference  exons
+     |    2 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=23141-31232
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01040
+|
+|  prediction genes:
+|    AT1G01040
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01040.1
+     |  prediction transcripts:
+     |    AT1G01040.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+ |
+     |  CDS structure comparison
+     |    12 reference  CDS segments
+     |    12 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    12 reference  exons
+     |    12 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    1 reference  UTR segments
+     |    1 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+============================================================
+========== ParsEval Summary
+============================================================
+
+Started:                31 Dec 2020, 08:38PM
+Reference annotations:  /tmp/tmpuaspc0eb/files/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat
+Prediction annotations: /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.dat
+Executing command:      parseval -l 5 -t 20 -w -f text -o /tmp/tmpuaspc0eb/files/9/2/0/dataset_92006ba5-932e-40f8-a785-2a9b2932d88a.dat /tmp/tmpuaspc0eb/files/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.dat 
+
+  Sequences compared
+    Chr1
+
+  Gene loci................................4
+    shared.................................4
+    unique to reference....................0
+    unique to prediction...................0
+
+  Reference annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Prediction annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Total comparisons........................5
+    perfect matches........................5 (100.0%)
+      avg. length..........................3617.40 bp
+      avg. # refr exons....................7.60
+      avg. # pred exons....................7.60
+      avg. refr CDS length.................449.40 aa
+      avg. pred CDS length.................449.40 aa
+    perfect matches with mislabeled UTRs...0 (0.0%)
+    CDS structure matches..................0 (0.0%)
+    exon structure matches.................0 (0.0%)
+    UTR structure matches..................0 (0.0%)
+    non-matches............................0 (0.0%)
+
+  CDS structure comparison
+    reference CDS segments.................35
+      match prediction.....................35 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction CDS segments................35
+      match reference......................35 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Exon structure comparison
+    reference exons........................38
+      match prediction.....................38 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction exons.......................38
+      match reference......................38 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  UTR structure comparison
+    reference UTR segments.................12
+      match prediction.....................12 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction UTR segments................12
+      match reference......................12 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Nucleotide-level comparison      CDS          UTRs         Overall   
+    Matching coefficient:          1.000        1.000        1.000
+    Correlation coefficient:       1.000        1.000        --        
+    Sensitivity:                   1.000        1.000        --        
+    Specificity:                   1.000        1.000        --        
+    F1 Score:                      1.000        1.000        --        
+    Annotation edit distance:      0.000        0.000        --        
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test2.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,577 @@
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=3631-5899
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01010
+|
+|  prediction genes:
+|    AT1G01010
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01010.1
+     |  prediction transcripts:
+     |    AT1G01010.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+ |
+     |  CDS structure comparison
+     |    6 reference  CDS segments
+     |    6 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    6 reference  exons
+     |    6 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    2 reference  UTR segments
+     |    2 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=5928-8737
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01020
+|
+|  prediction genes:
+|    AT1G01020
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.1
+     |  prediction transcripts:
+     |    AT1G01020.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+ |
+     |  CDS structure comparison
+     |    9 reference  CDS segments
+     |    9 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    10 reference  exons
+     |    10 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.2
+     |  prediction transcripts:
+     |    AT1G01020.2
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+ |
+     |  CDS structure comparison
+     |    7 reference  CDS segments
+     |    7 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    8 reference  exons
+     |    8 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=11649-13714
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01030
+|
+|  prediction genes:
+|    AT1G01030
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01030.1
+     |  prediction transcripts:
+     |    AT1G01030.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+ |
+     |  CDS structure comparison
+     |    1 reference  CDS segments
+     |    1 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    2 reference  exons
+     |    2 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=23146-31227
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01040
+|
+|  prediction genes:
+|    AT1G01040
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01040.1
+     |  prediction transcripts:
+     |    AT1G01040.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+ |
+     |  CDS structure comparison
+     |    12 reference  CDS segments
+     |    12 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    12 reference  exons
+     |    12 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    1 reference  UTR segments
+     |    1 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+============================================================
+========== ParsEval Summary
+============================================================
+
+Started:                31 Dec 2020, 08:38PM
+Reference annotations:  /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat
+Prediction annotations: /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat
+Executing command:      parseval -l 0 -t 32 -w -f text -o /tmp/tmpuaspc0eb/files/3/2/7/dataset_327cf1a1-a7ea-412e-ac0f-e23f78ff553a.dat /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat 
+
+  Sequences compared
+    Chr1
+
+  Gene loci................................4
+    shared.................................4
+    unique to reference....................0
+    unique to prediction...................0
+
+  Reference annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Prediction annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Total comparisons........................5
+    perfect matches........................5 (100.0%)
+      avg. length..........................3607.40 bp
+      avg. # refr exons....................7.60
+      avg. # pred exons....................7.60
+      avg. refr CDS length.................449.40 aa
+      avg. pred CDS length.................449.40 aa
+    perfect matches with mislabeled UTRs...0 (0.0%)
+    CDS structure matches..................0 (0.0%)
+    exon structure matches.................0 (0.0%)
+    UTR structure matches..................0 (0.0%)
+    non-matches............................0 (0.0%)
+
+  CDS structure comparison
+    reference CDS segments.................35
+      match prediction.....................35 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction CDS segments................35
+      match reference......................35 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Exon structure comparison
+    reference exons........................38
+      match prediction.....................38 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction exons.......................38
+      match reference......................38 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  UTR structure comparison
+    reference UTR segments.................12
+      match prediction.....................12 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction UTR segments................12
+      match reference......................12 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Nucleotide-level comparison      CDS          UTRs         Overall   
+    Matching coefficient:          1.000        1.000        1.000
+    Correlation coefficient:       1.000        1.000        --        
+    Sensitivity:                   1.000        1.000        --        
+    Specificity:                   1.000        1.000        --        
+    F1 Score:                      1.000        1.000        --        
+    Annotation edit distance:      0.000        0.000        --        
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test3.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,577 @@
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=3621-5913
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01010
+|
+|  prediction genes:
+|    AT1G01010
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01010.1
+     |  prediction transcripts:
+     |    AT1G01010.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+ |
+     |  CDS structure comparison
+     |    6 reference  CDS segments
+     |    6 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    6 reference  exons
+     |    6 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    2 reference  UTR segments
+     |    2 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=5914-8747
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01020
+|
+|  prediction genes:
+|    AT1G01020
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.1
+     |  prediction transcripts:
+     |    AT1G01020.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+ |
+     |  CDS structure comparison
+     |    9 reference  CDS segments
+     |    9 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    10 reference  exons
+     |    10 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.2
+     |  prediction transcripts:
+     |    AT1G01020.2
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+ |
+     |  CDS structure comparison
+     |    7 reference  CDS segments
+     |    7 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    8 reference  exons
+     |    8 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=11639-13724
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01030
+|
+|  prediction genes:
+|    AT1G01030
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01030.1
+     |  prediction transcripts:
+     |    AT1G01030.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+ |
+     |  CDS structure comparison
+     |    1 reference  CDS segments
+     |    1 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    2 reference  exons
+     |    2 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=23136-31237
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01040
+|
+|  prediction genes:
+|    AT1G01040
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01040.1
+     |  prediction transcripts:
+     |    AT1G01040.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+ |
+     |  CDS structure comparison
+     |    12 reference  CDS segments
+     |    12 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    12 reference  exons
+     |    12 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    1 reference  UTR segments
+     |    1 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+============================================================
+========== ParsEval Summary
+============================================================
+
+Started:                31 Dec 2020, 08:39PM
+Reference annotations:  /tmp/tmpuaspc0eb/files/a/5/5/dataset_a554f401-58a7-425c-88d9-4da452d77344.dat
+Prediction annotations: /tmp/tmpuaspc0eb/files/9/5/a/dataset_95aee753-49cb-406a-a66f-13f51ef7a287.dat
+Executing command:      parseval -l 10 -t 10 -w -f text -o /tmp/tmpuaspc0eb/files/f/7/e/dataset_f7ec07dd-99dc-47f5-b69e-b01cec68543f.dat /tmp/tmpuaspc0eb/files/a/5/5/dataset_a554f401-58a7-425c-88d9-4da452d77344.dat /tmp/tmpuaspc0eb/files/9/5/a/dataset_95aee753-49cb-406a-a66f-13f51ef7a287.dat 
+
+  Sequences compared
+    Chr1
+
+  Gene loci................................4
+    shared.................................4
+    unique to reference....................0
+    unique to prediction...................0
+
+  Reference annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Prediction annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Total comparisons........................5
+    perfect matches........................5 (100.0%)
+      avg. length..........................3629.80 bp
+      avg. # refr exons....................7.60
+      avg. # pred exons....................7.60
+      avg. refr CDS length.................449.40 aa
+      avg. pred CDS length.................449.40 aa
+    perfect matches with mislabeled UTRs...0 (0.0%)
+    CDS structure matches..................0 (0.0%)
+    exon structure matches.................0 (0.0%)
+    UTR structure matches..................0 (0.0%)
+    non-matches............................0 (0.0%)
+
+  CDS structure comparison
+    reference CDS segments.................35
+      match prediction.....................35 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction CDS segments................35
+      match reference......................35 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Exon structure comparison
+    reference exons........................38
+      match prediction.....................38 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction exons.......................38
+      match reference......................38 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  UTR structure comparison
+    reference UTR segments.................12
+      match prediction.....................12 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction UTR segments................12
+      match reference......................12 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Nucleotide-level comparison      CDS          UTRs         Overall   
+    Matching coefficient:          1.000        1.000        1.000
+    Correlation coefficient:       1.000        1.000        --        
+    Sensitivity:                   1.000        1.000        --        
+    Specificity:                   1.000        1.000        --        
+    F1 Score:                      1.000        1.000        --        
+    Annotation edit distance:      0.000        0.000        --        
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test4.html	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,146 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <title>ParsEval Summary</title>
+    <link rel="stylesheet" type="text/css" href="parseval.css" />
+    <script type="text/javascript" language="javascript" src="vendor/jquery.js"></script>
+    <script type="text/javascript" language="javascript" src="vendor/jquery.dataTables.js"></script>
+    <script type="text/javascript">
+      $(document).ready(function() {
+        $('#seqlist').dataTable( {
+          "sScrollY": "400px",
+          "bPaginate": false,
+          "bScrollCollapse": true,
+          "bSort": false,
+          "bFilter": false,
+          "bInfo": false
+        });
+      } );
+    </script>
+  </head>
+  <body>
+    <div id="content">
+      <h1>ParsEval Summary</h1>
+      <pre class="command">
+Started:                03 Jan 2021, 02:54PM
+Reference annotations:  /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat
+Prediction annotations: /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat
+Executing command:      parseval --delta 0 --maxtrans 32 -w -f html -o /tmp/tmpok6hen4l/job_working_directory/000/43/working/dataset_63abed3a-aaab-41d9-b66b-4030368d9362_files /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat </pre>
+
+      <h2>Sequences compared</h2>
+      <p class="indent">Click on a sequence ID below to see comparison results for individual loci.</p>
+      <table id="seqlist" class="indent">
+        <thead>
+          <tr>
+            <th>Sequence</th>
+            <th>Refr genes</th>
+            <th>Pred genes</th>
+            <th>Loci</th>
+          </tr>
+        </thead>
+        <tbody>
+        <tr><td><a href="Chr1/index.html">Chr1</a></td><td>4</td><td>4</td><td>4</td></tr>
+        </tbody>
+      </table>
+
+      <h2>Gene loci <span class="tooltip">[?]<span class="tooltip_text">If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See <a target="_blank" href="http://aegean.readthedocs.io/en/latest/loci.html">this page</a> for a formal definition of a locus annotation.</span></span></h2>
+      <table class="table_normal">
+        <tr><td>shared</td><td>4</td></tr>
+        <tr><td>unique to reference</td><td>0</td></tr>
+        <tr><td>unique to prediction</td><td>0</td></tr>
+        <tr><th class="right-align">Total</th><td>4</td></tr>
+      </table>
+
+      <h2>Reference annotations</h2>
+      <table class="table_normal">
+        <tr><td>genes</td><td>4</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
+        <tr><td>transcripts</td><td>5</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
+      </table>
+
+      <h2>Prediction annotations</h2>
+      <table class="table_normal">
+        <tr><td>genes</td><td>4</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
+        <tr><td>transcripts</td><td>5</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
+      </table>
+
+      <h2>Comparisons</h2>
+      <table class="comparisons">
+        <tr><th>Total comparisons</th><th>5</th></tr>
+        <tr><td><a href="perfectmatches.html">(+)</a> perfect matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.</span></span></td><td>5 (100.0%)</tr>
+        <tr class="cell_small"><td class="cell_indent">average length</td><td>3607.40 bp</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average # refr exons</td><td>7.60</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average # pred exons</td><td>7.60</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average refr CDS length</td><td>449.40 aa</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average pred CDS length</td><td>449.40 aa</td></tr>
+        <tr><td>(+) perfect matches with mislabeled UTRs <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) CDS structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) exon structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) UTR structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) non-matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Differences in CDS, exon, and UTR structure.</span></span></td><td>0 (0.0%)</tr>
+      </table>
+
+      <h3>CDS structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference CDS segments</td><td>35</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction CDS segments</td><td>35</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>Exon structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference exons</td><td>38</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction exons</td><td>38</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>UTR structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference UTR segments</td><td>12</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction UTR segments</td><td>12</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>Nucleotide-level comparison</h3>
+      <table class="table_wide table_extra_indent">
+        <tr><th>&nbsp;</th><th>CDS</th><th>UTRs</th><th>Overall</th></tr>
+        <tr><th class="left-align">matching coefficient</th><td>1.000</td><td>1.000</td><td>1.000</td></tr>
+        <tr><th class="left-align">correlation coefficient</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">sensitivity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">specificity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">F1 score</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">annotation edit distance</th><td>0.000</td><td>0.000</td><td>--</td></tr>
+      </table>
+
+      <p class="footer">
+        Generated by <a href="https://github.com/standage/AEGeAn/releases/tag/v0.16.0">AEGeAn v0.16.0 (stable )</a>.<br />
+        Copyright © 2016 <a href="http://aegean.readthedocs.io/en/latest/contrib.html">AEGeAn authors</a>.<br />
+        See <a href="LICENSE">LICENSE</a> for details.      </p>
+</div> </body> </html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test5.html	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,146 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <title>ParsEval Summary</title>
+    <link rel="stylesheet" type="text/css" href="parseval.css" />
+    <script type="text/javascript" language="javascript" src="vendor/jquery.js"></script>
+    <script type="text/javascript" language="javascript" src="vendor/jquery.dataTables.js"></script>
+    <script type="text/javascript">
+      $(document).ready(function() {
+        $('#seqlist').dataTable( {
+          "sScrollY": "400px",
+          "bPaginate": false,
+          "bScrollCollapse": true,
+          "bSort": false,
+          "bFilter": false,
+          "bInfo": false
+        });
+      } );
+    </script>
+  </head>
+  <body>
+    <div id="content">
+      <h1>ParsEval Summary</h1>
+      <pre class="command">
+Started:                03 Jan 2021, 02:54PM
+Reference annotations:  /tmp/tmpok6hen4l/files/3/2/4/dataset_324b4f7b-e4b1-45d0-a543-be63ae960b43.dat
+Prediction annotations: /tmp/tmpok6hen4l/files/b/4/0/dataset_b4066664-7777-4c30-9e37-820e44194617.dat
+Executing command:      parseval --delta 10 --maxtrans 10 -w -f html -o /tmp/tmpok6hen4l/job_working_directory/000/46/working/dataset_1f07132b-8f99-4a03-8305-5c4c5a68089c_files /tmp/tmpok6hen4l/files/3/2/4/dataset_324b4f7b-e4b1-45d0-a543-be63ae960b43.dat /tmp/tmpok6hen4l/files/b/4/0/dataset_b4066664-7777-4c30-9e37-820e44194617.dat </pre>
+
+      <h2>Sequences compared</h2>
+      <p class="indent">Click on a sequence ID below to see comparison results for individual loci.</p>
+      <table id="seqlist" class="indent">
+        <thead>
+          <tr>
+            <th>Sequence</th>
+            <th>Refr genes</th>
+            <th>Pred genes</th>
+            <th>Loci</th>
+          </tr>
+        </thead>
+        <tbody>
+        <tr><td><a href="Chr1/index.html">Chr1</a></td><td>4</td><td>4</td><td>4</td></tr>
+        </tbody>
+      </table>
+
+      <h2>Gene loci <span class="tooltip">[?]<span class="tooltip_text">If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See <a target="_blank" href="http://aegean.readthedocs.io/en/latest/loci.html">this page</a> for a formal definition of a locus annotation.</span></span></h2>
+      <table class="table_normal">
+        <tr><td>shared</td><td>4</td></tr>
+        <tr><td>unique to reference</td><td>0</td></tr>
+        <tr><td>unique to prediction</td><td>0</td></tr>
+        <tr><th class="right-align">Total</th><td>4</td></tr>
+      </table>
+
+      <h2>Reference annotations</h2>
+      <table class="table_normal">
+        <tr><td>genes</td><td>4</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
+        <tr><td>transcripts</td><td>5</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
+      </table>
+
+      <h2>Prediction annotations</h2>
+      <table class="table_normal">
+        <tr><td>genes</td><td>4</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
+        <tr><td>transcripts</td><td>5</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
+      </table>
+
+      <h2>Comparisons</h2>
+      <table class="comparisons">
+        <tr><th>Total comparisons</th><th>5</th></tr>
+        <tr><td><a href="perfectmatches.html">(+)</a> perfect matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.</span></span></td><td>5 (100.0%)</tr>
+        <tr class="cell_small"><td class="cell_indent">average length</td><td>3629.80 bp</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average # refr exons</td><td>7.60</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average # pred exons</td><td>7.60</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average refr CDS length</td><td>449.40 aa</td></tr>
+        <tr class="cell_small"><td class="cell_indent">average pred CDS length</td><td>449.40 aa</td></tr>
+        <tr><td>(+) perfect matches with mislabeled UTRs <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) CDS structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) exon structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) UTR structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.</span></span></td><td>0 (0.0%)</tr>
+        <tr><td>(+) non-matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Differences in CDS, exon, and UTR structure.</span></span></td><td>0 (0.0%)</tr>
+      </table>
+
+      <h3>CDS structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference CDS segments</td><td>35</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction CDS segments</td><td>35</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>Exon structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference exons</td><td>38</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction exons</td><td>38</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>UTR structure comparison</h3>
+      <table class="table_normal table_extra_indent">
+        <tr><td>reference UTR segments</td><td>12</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>prediction UTR segments</td><td>12</td></tr>
+        <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
+        <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
+        <tr><td>Sensitivity</td><td>1.000</td></tr>
+        <tr><td>Specificity</td><td>1.000</td></tr>
+        <tr><td>F1 score</td><td>1.000</td></tr>
+        <tr><td>Annotation edit distance</td><td>0.000</td></tr>
+      </table>
+
+      <h3>Nucleotide-level comparison</h3>
+      <table class="table_wide table_extra_indent">
+        <tr><th>&nbsp;</th><th>CDS</th><th>UTRs</th><th>Overall</th></tr>
+        <tr><th class="left-align">matching coefficient</th><td>1.000</td><td>1.000</td><td>1.000</td></tr>
+        <tr><th class="left-align">correlation coefficient</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">sensitivity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">specificity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">F1 score</th><td>1.000</td><td>1.000</td><td>--</td></tr>
+        <tr><th class="left-align">annotation edit distance</th><td>0.000</td><td>0.000</td><td>--</td></tr>
+      </table>
+
+      <p class="footer">
+        Generated by <a href="https://github.com/standage/AEGeAn/releases/tag/v0.16.0">AEGeAn v0.16.0 (stable )</a>.<br />
+        Copyright © 2016 <a href="http://aegean.readthedocs.io/en/latest/contrib.html">AEGeAn authors</a>.<br />
+        See <a href="LICENSE">LICENSE</a> for details.      </p>
+</div> </body> </html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test6.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,577 @@
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=3631-5899
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01010
+|
+|  prediction genes:
+|    AT1G01010
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01010.1
+     |  prediction transcripts:
+     |    AT1G01010.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+ |
+     |  CDS structure comparison
+     |    6 reference  CDS segments
+     |    6 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    6 reference  exons
+     |    6 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    2 reference  UTR segments
+     |    2 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=5928-8737
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01020
+|
+|  prediction genes:
+|    AT1G01020
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.1
+     |  prediction transcripts:
+     |    AT1G01020.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+ |
+     |  CDS structure comparison
+     |    9 reference  CDS segments
+     |    9 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    10 reference  exons
+     |    10 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.2
+     |  prediction transcripts:
+     |    AT1G01020.2
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+ |
+     |  CDS structure comparison
+     |    7 reference  CDS segments
+     |    7 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    8 reference  exons
+     |    8 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=11649-13714
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01030
+|
+|  prediction genes:
+|    AT1G01030
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01030.1
+     |  prediction transcripts:
+     |    AT1G01030.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+ |
+     |  CDS structure comparison
+     |    1 reference  CDS segments
+     |    1 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    2 reference  exons
+     |    2 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=23146-31227
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01040
+|
+|  prediction genes:
+|    AT1G01040
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01040.1
+     |  prediction transcripts:
+     |    AT1G01040.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+ |
+     |  CDS structure comparison
+     |    12 reference  CDS segments
+     |    12 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    12 reference  exons
+     |    12 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    1 reference  UTR segments
+     |    1 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+============================================================
+========== ParsEval Summary
+============================================================
+
+Started:                31 Dec 2020, 08:39PM
+Reference annotations:  example_ref_label
+Prediction annotations: example_pred_label
+Executing command:      parseval -l 0 -t 32 -w -x example_ref_label -y example_pred_label -f text -o /tmp/tmpuaspc0eb/files/1/7/a/dataset_17a21c9f-5e47-48fb-b467-1d022f11befc.dat /tmp/tmpuaspc0eb/files/2/d/4/dataset_2d46af81-606d-4a91-bdad-a08bfdbc2b2b.dat /tmp/tmpuaspc0eb/files/8/d/9/dataset_8d95a475-34f5-4968-a3a0-653b7a5efb86.dat 
+
+  Sequences compared
+    Chr1
+
+  Gene loci................................4
+    shared.................................4
+    unique to reference....................0
+    unique to prediction...................0
+
+  Reference annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Prediction annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Total comparisons........................5
+    perfect matches........................5 (100.0%)
+      avg. length..........................3607.40 bp
+      avg. # refr exons....................7.60
+      avg. # pred exons....................7.60
+      avg. refr CDS length.................449.40 aa
+      avg. pred CDS length.................449.40 aa
+    perfect matches with mislabeled UTRs...0 (0.0%)
+    CDS structure matches..................0 (0.0%)
+    exon structure matches.................0 (0.0%)
+    UTR structure matches..................0 (0.0%)
+    non-matches............................0 (0.0%)
+
+  CDS structure comparison
+    reference CDS segments.................35
+      match prediction.....................35 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction CDS segments................35
+      match reference......................35 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Exon structure comparison
+    reference exons........................38
+      match prediction.....................38 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction exons.......................38
+      match reference......................38 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  UTR structure comparison
+    reference UTR segments.................12
+      match prediction.....................12 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction UTR segments................12
+      match reference......................12 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Nucleotide-level comparison      CDS          UTRs         Overall   
+    Matching coefficient:          1.000        1.000        1.000
+    Correlation coefficient:       1.000        1.000        --        
+    Sensitivity:                   1.000        1.000        --        
+    Specificity:                   1.000        1.000        --        
+    F1 Score:                      1.000        1.000        --        
+    Annotation edit distance:      0.000        0.000        --