# HG changeset patch
# User bgruening
# Date 1694064564 0
# Node ID e009d8260be2323468792e65552fdf1d81c69430
# Parent  6d8444408ff139c2937ef9eaf9e0856e2a55f6a0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae

diff -r 6d8444408ff1 -r e009d8260be2 agat.xml
--- a/agat.xml	Tue May 23 18:05:26 2023 +0000
+++ b/agat.xml	Thu Sep 07 05:29:24 2023 +0000
@@ -9,19 +9,30 @@
     <command detect_errors="exit_code"><![CDATA[
         #if $tool.selector == 'fix'
             @input_annotation_single@
-            agat_convert_sp_gxf2gxf.pl -gff $input_annotation --output 'output.gff' &&
-            cat 'output.gff' > '${annotation_gff}'
+            agat_convert_sp_gxf2gxf.pl 
+                --gxf $input_annotation
+                --config $agat_configfile
+                --output 'output' &&
+            cat 'output' > '${annotation}'
         #else if $tool.selector == 'convert_GFF2GTF'
             @input_annotation_single@
-            agat_convert_sp_gff2gtf.pl --gff $input_annotation --gtf_version $tool.gtf_version --output 'output.gtf' &&
+            agat_convert_sp_gff2gtf.pl 
+                --gff $input_annotation 
+                --gtf_version $tool.gtf_version 
+                --output 'output.gtf' &&
             cat 'output.gtf' > '${annotation_gtf}'
         #else if $tool.selector == 'convert_GTF2GFF'
             @input_annotation_single@
-            agat_convert_sp_gxf2gxf.pl --gff $input_annotation --output 'output.gff' &&
+            agat_convert_sp_gxf2gxf.pl
+                --gff $input_annotation 
+                --output 'output.gff' &&
             cat 'output.gff' > '${annotation_gff}'
         #else if $tool.selector == 'compare'
             @input_annotation_double@
-            agat_sp_compare_two_annotations.pl --gff1 $input1 --gff2 $input2 --output 'temp_output' &&
+            agat_sp_compare_two_annotations.pl 
+                --gff1 $input1
+                --gff2 $input2
+                --output 'temp_output' &&
             cat 'temp_output' > '${stats_output}'
         #else if $tool.selector == 'extract'
             @input_annotation_single@
@@ -56,35 +67,100 @@
             @input_annotation_single@
             @input_reference@
             mkdir -p './statistics' &&
-            agat_sp_statistics.pl
+            agat_sp_functional_statistics.pl
             --gff $input_annotation
             --gs $ref_genome
             --output 'temp_output' &&
-            cat 'temp_output' > '$stats_output'
+            cat 'temp_output/gene@transcript/table_per_feature_type.txt' > '$stats_output'
+
         #else if  $tool.selector == 'merge_annotations'
             @input_annotation_double@
-            agat_sp_merge_annotations.pl -gff $input1 --gff $input2 --output 'temp_output' &&
-             cat 'temp_output' > '${annotation_gff}'
+            agat_sp_merge_annotations.pl 
+                --gff $input1
+                --gff $input2
+                --config $agat_configfile
+                --output 'output' &&
+             cat 'output' > '${annotation}'
         #else if $tool.selector == 'annotation_statistics'
             @input_annotation_single@
             @input_reference@
-            agat_sp_statistics.pl --gff $input_annotation --gs $ref_genome -d --output 'temp_output' &&
+            agat_sp_statistics.pl 
+                --gff $input_annotation 
+                --gs $ref_genome 
+                -d
+                --output 'temp_output' &&
             cat 'temp_output' > '$stats_output'
         #else if $tool.selector == 'filter_feature_fasta'
             @input_annotation_single@
             @input_reference@
-            agat_sq_filter_feature_from_fasta.pl --gff $input_annotation --fasta $ref_genome --output 'temp_output' &&
-            cat 'temp_output' > '${features_filtered}'
+            agat_sq_filter_feature_from_fasta.pl 
+                --gff $input_annotation 
+                --fasta $ref_genome 
+                --config $agat_configfile
+                --output 'output' &&
+                cat 'output' > '${annotation}'
         #else if $tool.selector == 'complement'
             @input_annotation_double@
-            agat_sp_complement_annotations.pl --ref $input1 --add $input2 --size_min $tool.size_min --output 'temp_output' &&
-            cat 'temp_output' > '${annotation_gff}'
+            agat_sp_complement_annotations.pl 
+                --ref $input1
+                --add $input2
+                --size_min $tool.size_min
+                --config $agat_configfile
+                --output 'temp_output' &&
+            cat 'temp_output' > '${annotation}'
+        #else if $tool.selector == 'splice_sites'
+            @input_annotation_single@
+            agat_sp_add_splice_sites.pl 
+                --gff $input_annotation
+                --config $agat_configfile
+                --output 'output' &&
+            cat 'output' > '${annotation}'
         #end if
         ]]>
     </command>
+        <configfiles>
+        <configfile name="agat_configfile"><![CDATA[
+#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta']
+---
+output_format: $tool.output_format.selector
+#if $tool.output_format.selector == "GFF"
+gff_output_version: $tool.output_format.version
+gtf_output_version: relax
+#else
+gff_output_version: 3
+gtf_output_version: $tool.output_format.version
+#end if
+verbose: 1
+progress_bar: true
+log: true
+debug: false
+tabix: false
+merge_loci: $tool.merge_loci
+throw_fasta: false
+force_gff_input_version: 0
+create_l3_for_l2_orphan: $tool.create_exon 
+locus_tag:
+- locus_tag
+- gene_id
+prefix_new_id: nbis
+check_sequential: true
+check_l2_linked_to_l3: true
+check_l1_linked_to_l2: true
+remove_orphan_l1: true
+check_all_level3_locations: true
+check_cds: true
+check_exons: true
+check_utrs: true
+check_all_level2_locations: true
+check_all_level1_locations: true
+check_identical_isoforms: true
+#end if
+        ]]></configfile>
+    </configfiles>
     <inputs>
         <conditional name="tool">
             <param name="selector" type="select" label="AGAT tool selector" help="As AGAT is a toolkit, it contains a lot of tools. If any of them is missing, please contact the server admin.">
+                <option value="splice_sites">Add splice sites</option>
                 <option value="annotation_statistics">Annotation statistics (agat_sp_statistics.pl)</option>
                 <option value="compare">Compare annotation files (agat_sp_compare_two_annotations.pl)</option>
                 <option value="complement">Complement annotation file (agat_sp_complement_annotations.pl)</option>
@@ -113,8 +189,8 @@
                     <option value="exon">Exon</option>
                     <option value="cds">CDS</option>
                     <option value="trna">tRNA</option>
-                    <option value="three_prime_utr">3' UTR</option>
-                    <option value="five_prime_utr">5' UTR</option>
+                    <option value="three_prime_utr">3 UTR</option>
+                    <option value="five_prime_utr">5 UTR</option>
                 </param>
                 <param argument="--mrna" type="boolean" truevalue="--mrna" falsevalue="" checked="false" label="Extract mRNA sequences" help=" This extract the mrna 
                     sequence (i.e transcribed sequence (devoid of introns, but containing untranslated exons))." />
@@ -127,7 +203,7 @@
                 <param argument="--clean_internal_stop" type="boolean" truevalue="--clean_internal_stop" falsevalue="" checked="false" label="Clean internal 
                     stop codons" help="The Clean Internal Stop option allows replacing the translation of the stop codons present among the sequence that is 
                     represented by the '*' character by . This character can be disturbing for many programs (e.g interproscan)" />
-                <param argument="--upstream" type="integer" min="0" value="" optional="true" label="Upstream nucleotides" help="It will take that number of nucleotide in more at the 5' extremity." />
+                <param argument="--upstream" type="integer" min="0" value="" optional="true" label="Upstream nucleotides" help="It will take that number of nucleotide in more at the 5 extremity." />
                 <param argument="--downstream" type="integer" min="0" value="" optional="true" label="Downstream nucleotides" help="It will take that number of downstream nucleotides." />
                 <param argument="--full" type="boolean" truevalue="--full" falsevalue="" checked="false" label="Full" help="This option allows dealing 
                     with feature that may span over several locations like CDS or exon, in order to extract the full sequence from the start extremity 
@@ -171,9 +247,11 @@
             <when value="filter_feature_fasta">
                 <expand macro="ANNOTATION_INPUT" />
                 <expand macro="REFERENCE_FASTA"/>
+                <expand macro="AGAT_CONFIG"/>
             </when>
             <when value="fix">
                 <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
+                <expand macro="AGAT_CONFIG"/>
             </when>
             <when value="functional_analysis">
                 <expand macro="ANNOTATION_INPUT" format="gff,gtf,gff3,gff3.gz"/>
@@ -182,24 +260,33 @@
             <when value="merge_annotations">
                 <param argument="--gff1" name="input_annotation1" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation file 1" help="Input GTF/GFF file" />
                 <param argument="--gff2" name="input_annotation2" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation file 2" help="Input GTF/GFF file" />
+                <expand macro="AGAT_CONFIG"/>
             </when>
             <when value="complement">
                 <param argument="--ref" name="input_annotation1" type="data" format="gff,gtf,gff3,gff3.gz" label="Reference annotaiton" help="Reference GTF/GFF file" />
                 <param argument="--add" name="input_annotation2" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation to complement" help="Annotation file you would like to use to complement the reference annotation." />
                 <param argument="--size_min" type="integer" min="0" value="0" label="Minimun CDS size" help="Option to keep the non-overlping gene only if the CDS size (in nucleotide) is over the minimum 
                     size defined. Default = 0 that means all of them are kept." />
+                <expand macro="AGAT_CONFIG"/>
+            </when>
+            <when value="splice_sites">
+                <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
+                <expand macro="AGAT_CONFIG"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
         <data name="annotation_gff" format="gff" label="${tool.name} on ${on_string}: annotation file (GFF)">
-            <filter>tool['selector'] not in ['annotation_statistics','extract','functional_analysis','compare','convert_GFF2GTF','filter_feature_fasta']</filter>
+            <filter>tool['selector'] == 'convert_GTF2GFF'</filter>
         </data>
         <data name="annotation_gtf" format="gtf" label="${tool.name} on ${on_string}: annotation file (GTF)">
             <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
         </data>
-        <data name="features_filtered" format="tabular" label="${tool.name} on ${on_string}: filtered results">
-            <filter>tool['selector'] == 'filter_feature_fasta'</filter>
+        <data name="annotation" format="gff" label="${tool.name} on ${on_string}: annotation file">
+            <filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff']</filter>
+            <change_format>
+                <when input="output_format.selector" value="GTF" format="gtf" />
+            </change_format>
         </data>
         <data name="sequence_output" format="fasta" label="${tool.name} on ${on_string}: FASTA file">
             <filter>tool['selector'] =='extract'</filter>
@@ -228,9 +315,6 @@
                 </conditional>
             </conditional>
             <output name="stats_output" file="test01_stats.txt" ftype="txt"/>
-            <output_collection name="distribution_plots_woiso" type="list" count="4">
-                <element name="transcriptClass_cds" file="test01_plot2.pdf" ftype="pdf" compare="sim_size" delta="100"/>
-            </output_collection>
             <output_collection name="distribution_plots_wiso" type="list" count="4">
                 <element name="transcriptClass_cds" file="test01_plot1.pdf" ftype="pdf" compare="sim_size" delta="100"/>
             </output_collection>
@@ -259,13 +343,17 @@
             </conditional>
             <output name="stats_output" file="test03.txt" ftype="txt" lines_diff="2"/>
         </test>
-        <!-- Test 04: comlement annotation -->
+        <!-- Test 04: complement annotation -->
         <test expect_num_outputs="1">
             <conditional name="tool">
                 <param name="selector" value="complement"/>
                 <param name="input_annotation1" value="annotation_small.gtf" ftype="gtf"/>
                 <param name="input_annotation2" value="annotation_unique.gtf" ftype="gtf"/>
                 <param name="size_min" value="10"/>
+                <conditional name="output_format">
+                    <param name="selector" value="gff"/>
+                    <param name="version" value="3"/>
+                </conditional>
             </conditional>
             <output name="annotation_gff" file="test04.gff" ftype="gff"/>
         </test>
@@ -296,7 +384,7 @@
                     <param name="history_item" value="genome.fasta.gz"/>
                 </conditional>
             </conditional>
-            <output name="features_filtered" file="test07.tabular" ftype="tabular"/>
+            <output name="annotation" file="test07.gff" ftype="gff"/>
         </test>
         <!-- Test 08: Fix annotation file -->
         <test expect_num_outputs="1">
@@ -328,6 +416,10 @@
                 <param name="input_annotation1" value="annotation_small.gtf"/>
                 <param name="input_annotation2" value="annotation_unique.gtf"/>
             </conditional>
+            <conditional name="output_format">
+                <param name="selector" value="gff"/>
+                <param name="version" value="3"/>
+            </conditional>
             <output name="annotation_gff" file="test10.gff" ftype="gff"/>
         </test>
         <!-- Test 11: Test compressed files -->
@@ -356,6 +448,14 @@
                 <has_text text="Job done" />
             </assert_stdout>
         </test>
+        <!-- Test 13: Add splicing sites -->
+        <test expect_num_outputs="1">
+            <conditional name="tool">
+                <param name="selector" value="splice_sites"/>
+                <param name="gff" value="test04.gff" ftype="gff"/>
+            </conditional>
+            <output name="annotation" file="test13.gff" ftype="gff"/>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 6d8444408ff1 -r e009d8260be2 macros.xml
--- a/macros.xml	Tue May 23 18:05:26 2023 +0000
+++ b/macros.xml	Thu Sep 07 05:29:24 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.2.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
@@ -19,7 +19,36 @@
     <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
         <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
     </xml>
-
+    <xml name="AGAT_CONFIG">
+        <conditional name="output_format">
+            <param name="selector" type="select" label="Output format">
+                <option value="GFF">GFF</option>
+                <option value="GTF">GTF</option>
+            </param>
+            <when value="GFF">
+                <param name="version" type="select" label="Format version">
+                    <option value="1">1</option>
+                    <option value="2">2</option>
+                    <option value="2.5">2.5</option>
+                    <option value="3" selected="true">3</option>
+                </param>
+            </when>
+            <when value="GTF">
+                <param name="version" type="select" label="Format version">
+                    <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option>
+                    <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option>
+                    <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option>
+                    <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option>
+                    <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option>
+                    <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option>
+                    <option value="relax" selected="true">Relax = All feature types will be accepted</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="merge_loci" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge loci" help="Should overlapping loci (at CDS level) be merged in a single locus. Only one gene is kept, and the mRNA features become isoforms." />
+        <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/>
+    </xml>
+    
     <xml name="REFERENCE_FASTA">
         <conditional name="reference_genome">
             <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
diff -r 6d8444408ff1 -r e009d8260be2 test-data/region.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/region.bed	Thu Sep 07 05:29:24 2023 +0000
@@ -0,0 +1,1 @@
+K03455	1	2669
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test01_plot1.pdf
Binary file test-data/test01_plot1.pdf has changed
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test01_plot2.pdf
Binary file test-data/test01_plot2.pdf has changed
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test01_stats.txt
--- a/test-data/test01_stats.txt	Tue May 23 18:05:26 2023 +0000
+++ b/test-data/test01_stats.txt	Thu Sep 07 05:29:24 2023 +0000
@@ -1,7 +1,6 @@
 --------------------------------------------------------------------------------
 
-Compute transcript with isoforms if any
-
+---------------------------------- transcript ----------------------------------
 Number of gene                               379
 Number of transcript                         379
 Number of cds                                376
@@ -14,67 +13,25 @@
 mean cdss per transcript                     1.0
 mean exons per transcript                    1.0
 mean exons per cds                           1.0
-Total gene length                            342644
-Total transcript length                      342644
-Total cds length                             342338
-Total exon length                            342644
-mean gene length                             904
-mean transcript length                       904
-mean cds length                              910
-mean exon length                             904
-mean cds piece length                        910
+Total gene length (bp)                       342644
+Total transcript length (bp)                 342644
+Total cds length (bp)                        342338
+Total exon length (bp)                       342644
+mean gene length (bp)                        904
+mean transcript length (bp)                  904
+mean cds length (bp)                         910
+mean exon length (bp)                        904
+mean cds piece length (bp)                   910
 % of genome covered by gene                  33.1
 % of genome covered by transcript            33.1
 % of genome covered by cds                   33.1
 % of genome covered by exon                  33.1
-Longest gene                                 9499
-Longest transcript                           9499
-Longest cds                                  9499
-Longest exon                                 9499
-Longest cds piece                            9499
-Shortest gene                                54
-Shortest transcript                          54
-Shortest cds                                 54
-Shortest exon                                54
-Shortest cds piece                           54
-
-Re-compute transcript without isoforms asked. We remove shortest isoforms if any
+Longest gene (bp)                            9499
+Longest transcript (bp)                      9499
+Longest cds (bp)                             9499
+Longest exon (bp)                            9499
+Longest cds piece (bp)                       9499
+Shortest gene (bp)                           54
+Shortest transcript (bp)                     54
+Shortest cds piece (bp)                      54
 
-Number of gene                               379
-Number of transcript                         379
-Number of cds                                376
-Number of exon                               379
-Number of exon in cds                        376
-Number gene overlapping                      62
-Number of single exon gene                   379
-Number of single exon transcript             379
-mean transcripts per gene                    1.0
-mean cdss per transcript                     1.0
-mean exons per transcript                    1.0
-mean exons per cds                           1.0
-Total gene length                            342644
-Total transcript length                      342644
-Total cds length                             342338
-Total exon length                            342644
-mean gene length                             904
-mean transcript length                       904
-mean cds length                              910
-mean exon length                             904
-mean cds piece length                        910
-% of genome covered by gene                  33.1
-% of genome covered by transcript            33.1
-% of genome covered by cds                   33.1
-% of genome covered by exon                  33.1
-Longest gene                                 9499
-Longest transcript                           9499
-Longest cds                                  9499
-Longest exon                                 9499
-Longest cds piece                            9499
-Shortest gene                                54
-Shortest transcript                          54
-Shortest cds                                 54
-Shortest exon                                54
-Shortest cds piece                           54
-
---------------------------------------------------------------------------------
-
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test03.txt
--- a/test-data/test03.txt	Tue May 23 18:05:26 2023 +0000
+++ b/test-data/test03.txt	Thu Sep 07 05:29:24 2023 +0000
@@ -1,4 +1,4 @@
-usage: /home/laptop/miniconda3/envs/mulled-v1-d5d9956f5cc87a70e05e5aa3970eaf3637ef7e96fa1e50da0f6646fabcdc59e1/bin/agat_sp_compare_two_annotations.pl --gff1 annotation1.gtf --gff2 annotation2.gtf --output temp_output
+usage: /home/laptop/miniconda3/envs/__agat@1.2.0/bin/agat_sp_compare_two_annotations.pl --gff1 annotation1.gtf --gff2 annotation2.gtf --output temp_output
 Results of number of genes from file1 that overlap genes from file2:
 
 ----------------------------------------------------------------------------------------------
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test07.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test07.gff	Thu Sep 07 05:29:24 2023 +0000
@@ -0,0 +1,41 @@
+##gff-version 3
+NZ_CP027599.1	RefSeq	gene	1052	2152	.	+	.	ID=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010
+NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	ID=gene-C7A06_RS00010;Parent=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010;original_biotype=mrna;transcript_id=gene-C7A06_RS00010
+NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	ID=nbis-exon-2;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1;locus_tag=C7A06_RS00010;product=DNA polymerase III subunit beta;protein_id=WP_000673464.1;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	ID=cds-WP_000673464.1;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1;locus_tag=C7A06_RS00010;product=DNA polymerase III subunit beta;protein_id=WP_000673464.1;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	RefSeq	gene	2152	3225	.	+	.	ID=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015
+NZ_CP027599.1	RefSeq	transcript	2152	3225	.	+	.	ID=gene-C7A06_RS00015;Parent=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015;original_biotype=mrna;transcript_id=gene-C7A06_RS00015
+NZ_CP027599.1	Protein Homology	exon	2152	3225	.	+	.	ID=nbis-exon-3;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	2152	3225	.	+	0	ID=cds-WP_000060112.1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	RefSeq	gene	3254	5668	.	+	.	ID=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020
+NZ_CP027599.1	RefSeq	transcript	3254	5668	.	+	.	ID=gene-C7A06_RS00020;Parent=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020;original_biotype=mrna;transcript_id=gene-C7A06_RS00020
+NZ_CP027599.1	Protein Homology	exon	3254	5668	.	+	.	ID=nbis-exon-4;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	3254	5668	.	+	0	ID=cds-WP_000072067.1;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	RefSeq	gene	5908	6306	.	+	.	ID=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025
+NZ_CP027599.1	RefSeq	transcript	5908	6306	.	+	.	ID=gene-C7A06_RS00025;Parent=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025;original_biotype=mrna;transcript_id=gene-C7A06_RS00025
+NZ_CP027599.1	Protein Homology	exon	5908	6306	.	+	.	ID=nbis-exon-5;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	5908	6306	.	+	0	ID=cds-WP_000522208.1;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	RefSeq	gene	6421	7233	.	+	.	ID=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030
+NZ_CP027599.1	RefSeq	transcript	6421	7233	.	+	.	ID=gene-C7A06_RS00030;Parent=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030;original_biotype=mrna;transcript_id=gene-C7A06_RS00030
+NZ_CP027599.1	Protein Homology	exon	6421	7233	.	+	.	ID=nbis-exon-6;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418152.1;locus_tag=C7A06_RS00030;product=sugar-phosphatase;protein_id=WP_000985541.1;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	6421	7233	.	+	0	ID=cds-WP_000985541.1;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418152.1;locus_tag=C7A06_RS00030;product=sugar-phosphatase;protein_id=WP_000985541.1;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	RefSeq	gene	7279	7935	.	-	.	ID=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035
+NZ_CP027599.1	RefSeq	transcript	7279	7935	.	-	.	ID=gene-C7A06_RS00035;Parent=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035
+NZ_CP027599.1	Protein Homology	exon	7279	7935	.	-	.	ID=nbis-exon-7;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	7279	7935	.	-	0	ID=cds-WP_000772931.1;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8213	8902	.	+	.	ID=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040
+NZ_CP027599.1	RefSeq	transcript	8213	8902	.	+	.	ID=gene-C7A06_RS00040;Parent=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040;original_biotype=mrna;transcript_id=gene-C7A06_RS00040
+NZ_CP027599.1	Protein Homology	exon	8213	8902	.	+	.	ID=nbis-exon-8;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8213	8902	.	+	0	ID=cds-WP_000174305.1;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8899	9777	.	+	.	ID=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045
+NZ_CP027599.1	RefSeq	transcript	8899	9777	.	+	.	ID=gene-C7A06_RS00045;Parent=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045;original_biotype=mrna;transcript_id=gene-C7A06_RS00045
+NZ_CP027599.1	Protein Homology	exon	8899	9777	.	+	.	ID=nbis-exon-9;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8899	9777	.	+	0	ID=cds-WP_000127112.1;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	RefSeq	gene	9761	10378	.	+	.	ID=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050
+NZ_CP027599.1	RefSeq	transcript	9761	10378	.	+	.	ID=gene-C7A06_RS00050;Parent=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050;original_biotype=mrna;transcript_id=gene-C7A06_RS00050
+NZ_CP027599.1	Protein Homology	exon	9761	10378	.	+	.	ID=nbis-exon-10;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;inference=COORDINATES: similar to AA sequence:RefSeq:YP_026238.1;locus_tag=C7A06_RS00050;product=2-dehydro-3-deoxy-6-phosphogalactonate aldolase;protein_id=WP_001198699.1;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	9761	10378	.	+	0	ID=cds-WP_001198699.1;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;inference=COORDINATES: similar to AA sequence:RefSeq:YP_026238.1;locus_tag=C7A06_RS00050;product=2-dehydro-3-deoxy-6-phosphogalactonate aldolase;protein_id=WP_001198699.1;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	RefSeq	gene	10375	11523	.	+	.	ID=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055
+NZ_CP027599.1	RefSeq	transcript	10375	11523	.	+	.	ID=gene-C7A06_RS00055;Parent=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055;original_biotype=mrna;transcript_id=gene-C7A06_RS00055
+NZ_CP027599.1	Protein Homology	exon	10375	11523	.	+	.	ID=nbis-exon-11;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;go_function=galactonate dehydratase activity|0008869||IEA;go_process=cellular amino acid catabolic process|0009063||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1;locus_tag=C7A06_RS00055;product=galactonate dehydratase;protein_id=WP_000705001.1;transcript_id=gene-C7A06_RS00055;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	10375	11523	.	+	0	ID=cds-WP_000705001.1;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;go_function=galactonate dehydratase activity|0008869||IEA;go_process=cellular amino acid catabolic process|0009063||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1;locus_tag=C7A06_RS00055;product=galactonate dehydratase;protein_id=WP_000705001.1;transcript_id=gene-C7A06_RS00055;transl_table=11
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test07.tabular
--- a/test-data/test07.tabular	Tue May 23 18:05:26 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-##gff-version 3
-NZ_CP027599.1	RefSeq	gene	1052	2152	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	
-NZ_CP027599.1	RefSeq	gene	2152	3225	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	2152	3225	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	2152	3225	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	2152	3225	.	+	0	
-NZ_CP027599.1	RefSeq	gene	3254	5668	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	3254	5668	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	3254	5668	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	3254	5668	.	+	0	
-NZ_CP027599.1	RefSeq	gene	5908	6306	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	5908	6306	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	5908	6306	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	5908	6306	.	+	0	
-NZ_CP027599.1	RefSeq	gene	6421	7233	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	6421	7233	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	6421	7233	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	6421	7233	.	+	0	
-NZ_CP027599.1	RefSeq	gene	7279	7935	.	-	.	
-NZ_CP027599.1	RefSeq	transcript	7279	7935	.	-	.	
-NZ_CP027599.1	Protein Homology	exon	7279	7935	.	-	.	
-NZ_CP027599.1	Protein Homology	CDS	7279	7935	.	-	0	
-NZ_CP027599.1	RefSeq	gene	8213	8902	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	8213	8902	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	8213	8902	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	8213	8902	.	+	0	
-NZ_CP027599.1	RefSeq	gene	8899	9777	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	8899	9777	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	8899	9777	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	8899	9777	.	+	0	
-NZ_CP027599.1	RefSeq	gene	9761	10378	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	9761	10378	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	9761	10378	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	9761	10378	.	+	0	
-NZ_CP027599.1	RefSeq	gene	10375	11523	.	+	.	
-NZ_CP027599.1	RefSeq	transcript	10375	11523	.	+	.	
-NZ_CP027599.1	Protein Homology	exon	10375	11523	.	+	.	
-NZ_CP027599.1	Protein Homology	CDS	10375	11523	.	+	0	
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test09.txt
--- a/test-data/test09.txt	Tue May 23 18:05:26 2023 +0000
+++ b/test-data/test09.txt	Thu Sep 07 05:29:24 2023 +0000
@@ -1,80 +1,131 @@
---------------------------------------------------------------------------------
 
-Compute transcript with isoforms if any
-
-Number of gene                               10
-Number of transcript                         10
-Number of cds                                10
-Number of exon                               10
-Number of exon in cds                        10
-Number gene overlapping                      4
-Number of single exon gene                   10
-Number of single exon transcript             10
-mean transcripts per gene                    1.0
-mean cdss per transcript                     1.0
-mean exons per transcript                    1.0
-mean exons per cds                           1.0
-Total gene length                            9795
-Total transcript length                      9795
-Total cds length                             9795
-Total exon length                            9795
-mean gene length                             979
-mean transcript length                       979
-mean cds length                              979
-mean exon length                             979
-mean cds piece length                        979
-% of genome covered by gene                  0.9
-% of genome covered by transcript            0.9
-% of genome covered by cds                   0.9
-% of genome covered by exon                  0.9
-Longest gene                                 2415
-Longest transcript                           2415
-Longest cds                                  2415
-Longest exon                                 2415
-Longest cds piece                            2415
-Shortest gene                                399
-Shortest transcript                          399
-Shortest cds                                 399
-Shortest exon                                399
-Shortest cds piece                           399
-
-Re-compute transcript without isoforms asked. We remove shortest isoforms if any
-
-Number of gene                               10
-Number of transcript                         10
-Number of cds                                10
-Number of exon                               10
-Number of exon in cds                        10
-Number gene overlapping                      4
-Number of single exon gene                   10
-Number of single exon transcript             10
-mean transcripts per gene                    1.0
-mean cdss per transcript                     1.0
-mean exons per transcript                    1.0
-mean exons per cds                           1.0
-Total gene length                            9795
-Total transcript length                      9795
-Total cds length                             9795
-Total exon length                            9795
-mean gene length                             979
-mean transcript length                       979
-mean cds length                              979
-mean exon length                             979
-mean cds piece length                        979
-% of genome covered by gene                  0.9
-% of genome covered by transcript            0.9
-% of genome covered by cds                   0.9
-% of genome covered by exon                  0.9
-Longest gene                                 2415
-Longest transcript                           2415
-Longest cds                                  2415
-Longest exon                                 2415
-Longest cds piece                            2415
-Shortest gene                                399
-Shortest transcript                          399
-Shortest cds                                 399
-Shortest exon                                399
-Shortest cds piece                           399
-
---------------------------------------------------------------------------------
-
+Functional info gene@transcript records:
+ _____________________________________________________________________________
+|                         |      Nb holded by       |         Nb gene         |
+|                         |          gene           |        holding it       |
+|_____________________________________________________________________________|
+|          name           |            10           |            10           |
+|_____________________________________________________________________________|
+|         product         |            0            |            0            |
+|_____________________________________________________________________________|
+|       description       |            0            |            0            |
+|_____________________________________________________________________________|
+|      ontology_term      |            0            |            0            |
+|_____________________________________________________________________________|
+|          dbxref         |            0            |            0            |
+|_____________________________________________________________________________|
+|      dbxref:Genbank     |            0            |            0            |
+|_____________________________________________________________________________|
+Nb gene = 10
+Nb gene with <name> attribute = 10
+Nb gene without <name> attribute = 0
+Nb gene with <product> attribute = 0
+Nb gene without <product> attribute = 10
+Nb gene with <description> attribute = 0
+Nb gene without <description> attribute = 10
+Nb gene with <ontology_term> attribute = 0
+Nb gene without <ontology_term> attribute = 10
+Nb gene with <dbxref> attribute = 0
+Nb gene without <dbxref> attribute = 10
+Nb gene with <Genbank> dbxref = 0
+Nb gene without <Genbank> dbxref = 10
+ _______________________________________________________________________________________________________
+|                         |      Nb holded by       |      Nb transcript      |      Nb gene with       |
+|                         |        transcript       |        holding it       |  transcript holding it  |
+|_______________________________________________________________________________________________________|
+|          name           |            10           |            10           |            10           |
+|_______________________________________________________________________________________________________|
+|         product         |            0            |            0            |            0            |
+|_______________________________________________________________________________________________________|
+|       description       |            0            |            0            |            0            |
+|_______________________________________________________________________________________________________|
+|      ontology_term      |            0            |            0            |            0            |
+|_______________________________________________________________________________________________________|
+|          dbxref         |            0            |            0            |            0            |
+|_______________________________________________________________________________________________________|
+|      dbxref:Genbank     |            0            |            0            |            0            |
+|_______________________________________________________________________________________________________|
+Nb gene = 10
+Nb transcript = 10
+Nb gene with <name> attribute = 10
+Nb gene without <name> attribute = 0
+Nb transcript with <name> attribute = 10
+Nb transcript without <name> attribute = 0
+Nb gene with <product> attribute = 0
+Nb gene without <product> attribute = 10
+Nb transcript with <product> attribute = 0
+Nb transcript without <product> attribute = 10
+Nb gene with <description> attribute = 0
+Nb gene without <description> attribute = 10
+Nb transcript with <description> attribute = 0
+Nb transcript without <description> attribute = 10
+Nb gene with <ontology_term> attribute = 0
+Nb gene without <ontology_term> attribute = 10
+Nb transcript with <ontology_term> attribute = 0
+Nb transcript without <ontology_term> attribute = 10
+Nb gene with <dbxref> attribute = 0
+Nb gene without <dbxref> attribute = 10
+Nb transcript with <dbxref> attribute = 0
+Nb transcript without <dbxref> attribute = 10
+Nb gene with Genbank dbxref = 0
+Nb gene without Genbank dbxref = 10
+Nb transcript with Genbank dbxref = 0
+Nb transcript without Genbank dbxref = 10
+ _____________________________________________________________________________
+|                         |      Nb holded by       |          Nb cds         |
+|                         |           cds           |        holding it       |
+|_____________________________________________________________________________|
+|          name           |            10           |            10           |
+|_____________________________________________________________________________|
+|         product         |            10           |            10           |
+|_____________________________________________________________________________|
+|       description       |            0            |            0            |
+|_____________________________________________________________________________|
+|      ontology_term      |            12           |            5            |
+|_____________________________________________________________________________|
+|          dbxref         |            10           |            10           |
+|_____________________________________________________________________________|
+|      dbxref:Genbank     |            10           |            10           |
+|_____________________________________________________________________________|
+Nb cds = 10
+Nb cds with <name> attribute = 10
+Nb cds without <name> attribute = 0
+Nb cds with <product> attribute = 10
+Nb cds without <product> attribute = 0
+Nb cds with <description> attribute = 0
+Nb cds without <description> attribute = 10
+Nb cds with <ontology_term> attribute = 5
+Nb cds without <ontology_term> attribute = 5
+Nb cds with <dbxref> attribute = 10
+Nb cds without <dbxref> attribute = 0
+Nb cds with <Genbank> dbxref = 10
+Nb cds without <Genbank> dbxref = 0
+ _____________________________________________________________________________
+|                         |      Nb holded by       |         Nb exon         |
+|                         |          exon           |        holding it       |
+|_____________________________________________________________________________|
+|          name           |            10           |            10           |
+|_____________________________________________________________________________|
+|         product         |            10           |            10           |
+|_____________________________________________________________________________|
+|       description       |            0            |            0            |
+|_____________________________________________________________________________|
+|      ontology_term      |            12           |            5            |
+|_____________________________________________________________________________|
+|          dbxref         |            10           |            10           |
+|_____________________________________________________________________________|
+|      dbxref:Genbank     |            10           |            10           |
+|_____________________________________________________________________________|
+Nb exon = 10
+Nb exon with <name> attribute = 10
+Nb exon without <name> attribute = 0
+Nb exon with <product> attribute = 10
+Nb exon without <product> attribute = 0
+Nb exon with <description> attribute = 0
+Nb exon without <description> attribute = 10
+Nb exon with <ontology_term> attribute = 5
+Nb exon without <ontology_term> attribute = 5
+Nb exon with <dbxref> attribute = 10
+Nb exon without <dbxref> attribute = 0
+Nb exon with <Genbank> dbxref = 10
+Nb exon without <Genbank> dbxref = 0
diff -r 6d8444408ff1 -r e009d8260be2 test-data/test13.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test13.gff	Thu Sep 07 05:29:24 2023 +0000
@@ -0,0 +1,54 @@
+##gff-version 3
+##gtf-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM301845v1
+#!genome-build-accession NCBI_Assembly:GCF_003018455.1
+#!annotation-date 05/25/2022 04:54:31
+#!annotation-source NCBI RefSeq 
+##sequence-region NZ_CP027599.1 1 5942969
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562
+NZ_CP027599.1	RefSeq	gene	1052	2152	.	+	.	ID=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010
+NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	ID=gene-C7A06_RS00010;Parent=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010;original_biotype=mrna;transcript_id=gene-C7A06_RS00010
+NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	ID=nbis-exon-2;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1;locus_tag=C7A06_RS00010;product=DNA polymerase III subunit beta;protein_id=WP_000673464.1;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	ID=cds-WP_000673464.1;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1;locus_tag=C7A06_RS00010;product=DNA polymerase III subunit beta;protein_id=WP_000673464.1;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	RefSeq	gene	2152	3225	.	+	.	ID=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015
+NZ_CP027599.1	RefSeq	transcript	2152	3225	.	+	.	ID=gene-C7A06_RS00015;Parent=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015;original_biotype=mrna;transcript_id=gene-C7A06_RS00015
+NZ_CP027599.1	Protein Homology	exon	2152	3225	.	+	.	ID=nbis-exon-3;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	2152	3225	.	+	0	ID=cds-WP_000060112.1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	RefSeq	gene	3254	5668	.	+	.	ID=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020
+NZ_CP027599.1	RefSeq	transcript	3254	5668	.	+	.	ID=gene-C7A06_RS00020;Parent=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020;original_biotype=mrna;transcript_id=gene-C7A06_RS00020
+NZ_CP027599.1	Protein Homology	exon	3254	5668	.	+	.	ID=nbis-exon-4;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	3254	5668	.	+	0	ID=cds-WP_000072067.1;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	RefSeq	gene	5908	6306	.	+	.	ID=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025
+NZ_CP027599.1	RefSeq	transcript	5908	6306	.	+	.	ID=gene-C7A06_RS00025;Parent=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025;original_biotype=mrna;transcript_id=gene-C7A06_RS00025
+NZ_CP027599.1	Protein Homology	exon	5908	6306	.	+	.	ID=nbis-exon-5;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	5908	6306	.	+	0	ID=cds-WP_000522208.1;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	RefSeq	gene	6421	7233	.	+	.	ID=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030
+NZ_CP027599.1	RefSeq	transcript	6421	7233	.	+	.	ID=gene-C7A06_RS00030;Parent=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030;original_biotype=mrna;transcript_id=gene-C7A06_RS00030
+NZ_CP027599.1	Protein Homology	exon	6421	7233	.	+	.	ID=nbis-exon-6;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418152.1;locus_tag=C7A06_RS00030;product=sugar-phosphatase;protein_id=WP_000985541.1;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	6421	7233	.	+	0	ID=cds-WP_000985541.1;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418152.1;locus_tag=C7A06_RS00030;product=sugar-phosphatase;protein_id=WP_000985541.1;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	RefSeq	gene	7279	7935	.	-	.	ID=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035
+NZ_CP027599.1	RefSeq	transcript	7279	7935	.	-	.	ID=gene-C7A06_RS00035;Parent=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035
+NZ_CP027599.1	Protein Homology	exon	7279	7935	.	-	.	ID=nbis-exon-7;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	7279	7935	.	-	0	ID=cds-WP_000772931.1;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8213	8902	.	+	.	ID=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040
+NZ_CP027599.1	RefSeq	transcript	8213	8902	.	+	.	ID=gene-C7A06_RS00040;Parent=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040;original_biotype=mrna;transcript_id=gene-C7A06_RS00040
+NZ_CP027599.1	Protein Homology	exon	8213	8902	.	+	.	ID=nbis-exon-8;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8213	8902	.	+	0	ID=cds-WP_000174305.1;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8899	9777	.	+	.	ID=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045
+NZ_CP027599.1	RefSeq	transcript	8899	9777	.	+	.	ID=gene-C7A06_RS00045;Parent=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045;original_biotype=mrna;transcript_id=gene-C7A06_RS00045
+NZ_CP027599.1	Protein Homology	exon	8899	9777	.	+	.	ID=nbis-exon-9;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8899	9777	.	+	0	ID=cds-WP_000127112.1;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	RefSeq	gene	9761	10378	.	+	.	ID=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050
+NZ_CP027599.1	RefSeq	transcript	9761	10378	.	+	.	ID=gene-C7A06_RS00050;Parent=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050;original_biotype=mrna;transcript_id=gene-C7A06_RS00050
+NZ_CP027599.1	Protein Homology	exon	9761	10378	.	+	.	ID=nbis-exon-10;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;inference=COORDINATES: similar to AA sequence:RefSeq:YP_026238.1;locus_tag=C7A06_RS00050;product=2-dehydro-3-deoxy-6-phosphogalactonate aldolase;protein_id=WP_001198699.1;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	9761	10378	.	+	0	ID=cds-WP_001198699.1;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;inference=COORDINATES: similar to AA sequence:RefSeq:YP_026238.1;locus_tag=C7A06_RS00050;product=2-dehydro-3-deoxy-6-phosphogalactonate aldolase;protein_id=WP_001198699.1;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	RefSeq	gene	10375	11523	.	+	.	ID=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055
+NZ_CP027599.1	RefSeq	transcript	10375	11523	.	+	.	ID=gene-C7A06_RS00055;Parent=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055;original_biotype=mrna;transcript_id=gene-C7A06_RS00055
+NZ_CP027599.1	Protein Homology	exon	10375	11523	.	+	.	ID=nbis-exon-11;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;go_function=galactonate dehydratase activity|0008869||IEA;go_process=cellular amino acid catabolic process|0009063||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1;locus_tag=C7A06_RS00055;product=galactonate dehydratase;protein_id=WP_000705001.1;transcript_id=gene-C7A06_RS00055;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	10375	11523	.	+	0	ID=cds-WP_000705001.1;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;go_function=galactonate dehydratase activity|0008869||IEA;go_process=cellular amino acid catabolic process|0009063||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1;locus_tag=C7A06_RS00055;product=galactonate dehydratase;protein_id=WP_000705001.1;transcript_id=gene-C7A06_RS00055;transl_table=11
+NZ_CP027599.1	RefSeq	gene	11598	12935	.	+	.	ID=nbis-gene-12;Name=dgoT;gbkey=Gene;gene=dgoT;gene_biotype=protein_coding;gene_id=nbis-gene-12;locus_tag=C7A06_RS00060
+NZ_CP027599.1	RefSeq	transcript	11598	12935	.	+	.	ID=gene-C7A06_RS00060;Parent=nbis-gene-12;Name=dgoT;gbkey=Gene;gene=dgoT;gene_biotype=protein_coding;gene_id=nbis-gene-12;locus_tag=C7A06_RS00060;original_biotype=mrna;transcript_id=gene-C7A06_RS00060
+NZ_CP027599.1	Protein Homology	exon	11598	12935	.	+	.	ID=nbis-exon-12;Parent=gene-C7A06_RS00060;Dbxref=Genbank:WP_000253455.1;Name=WP_000253455.1;gbkey=CDS;gene=dgoT;gene_id=nbis-gene-12;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709507.1;locus_tag=C7A06_RS00060;product=MFS transporter;protein_id=WP_000253455.1;transcript_id=gene-C7A06_RS00060;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	11598	12935	.	+	0	ID=cds-WP_000253455.1;Parent=gene-C7A06_RS00060;Dbxref=Genbank:WP_000253455.1;Name=WP_000253455.1;gbkey=CDS;gene=dgoT;gene_id=nbis-gene-12;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709507.1;locus_tag=C7A06_RS00060;product=MFS transporter;protein_id=WP_000253455.1;transcript_id=gene-C7A06_RS00060;transl_table=11