Mercurial > repos > iuc > ncbi_datasets

changeset 5:6c829a430475 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
author iuc
date Wed, 04 May 2022 13:15:43 +0000
parents c47a0a93ffd2
children 5a2656cc84cb
files datasets_genome.xml macros.xml test-data/GCF_000001405.40.seq.rpt.jsonl test-data/GCF_000007445.1.genomic.gtf test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl test-data/genome.2.GCF_000013305.1.genomic.gtf test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl test-data/genome.3.GCF_000007445.1.genomic.gbff test-data/genome.3.GCF_000007445.1.genomic.gff test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl test-data/genome.3.GCF_000013305.1.genomic.gbff test-data/genome.3.GCF_000013305.1.genomic.gff test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl
diffstat 13 files changed, 262 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/datasets_genome.xml	Mon Mar 07 12:05:56 2022 +0000
+++ b/datasets_genome.xml	Wed May 04 13:15:43 2022 +0000
@@ -19,10 +19,10 @@
 $filters.reference
 $filters.annotated
 #if $filters.assembly_level:
---assembly_level $filters.assembly_level
+--assembly-level $filters.assembly_level
 #end if
 #if $filters.assembly_source:
---assembly_source $filters.assembly_source
+--assembly-source $filters.assembly_source
 #end if
 #if $filters.chromosomes:
 --chromosomes '$filters.chromosomes'
@@ -68,7 +68,7 @@
                 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/>
             </repeat>
         </section>
-        <section name="file_choices" title="File Choices">
+        <section name="file_choices" title="File Choices" expanded="true">
             <expand macro="excludes_genome"></expand>
             <expand macro="includes_genome"></expand>
         </section>
@@ -90,23 +90,23 @@
         </collection>
         <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/.*(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
-            <filter>uncompressed and file_choices['exclude_seq']</filter>
+            <filter>uncompressed and not file_choices['exclude_seq']</filter>
         </collection>
         <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
-            <filter>uncompressed and file_choices['exclude_genomic_cds']</filter>
+            <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter>
         </collection>
         <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
-            <filter>uncompressed and file_choices['exclude_gff3']</filter>
+            <filter>uncompressed and not file_choices['exclude_gff3']</filter>
         </collection>
         <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
-            <filter>uncompressed and file_choices['exclude_rna']</filter>
+            <filter>uncompressed and not file_choices['exclude_rna']</filter>
         </collection>
         <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
-            <filter>uncompressed and file_choices['exclude_protein']</filter>
+            <filter>uncompressed and not file_choices['exclude_protein']</filter>
         </collection>
         <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
@@ -125,6 +125,11 @@
                 <param name="taxon" value="human"></param>
             </conditional>
             <param name="chromosomes" value="21"></param>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="true"/>
+            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_gff3" value="true"/>
             <param name="uncompressed" value="false"/>
             <param name="released_before" value="01/01/2018"></param>
             <output name="archive_contents">
@@ -133,7 +138,28 @@
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="2">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="taxon"></param>
+                <param name="text_or_file" value="text"></param>
+                <param name="taxon" value="human"></param>
+            </conditional>
+            <param name="chromosomes" value="21"></param>
+            <param name="uncompressed" value="false"/>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="true"/>
+            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_gff3" value="true"/>
+            <param name="assembly_level" value="chromosome"/>
+            <param name="released_before" value="01/01/2018"></param>
+            <output name="archive_contents">
+                <assert_contents>
+                    <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="4">
             <conditional name="query|subcommand">
                 <param name="download_by" value="accession"></param>
                 <conditional name="text_or_file">
@@ -143,17 +169,16 @@
             </conditional>
             <param name="uncompressed" value="true"/>
             <param name="released_before" value="01/01/2007"></param>
-            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="true"/>
+            <param name="exclude_gff3" value="true"/>
             <param name="include_gtf" value="true"/>
             <output name="genome_data_report">
                 <assert_contents>
                     <has_text text="GCF_000013305.1"/>
                 </assert_contents>
             </output>
-            <output_collection name="sequence_report" type="list">
-                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
-                <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
-            </output_collection>
             <output_collection name="genomic_gtf" type="list">
                 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
                 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
@@ -172,8 +197,10 @@
                 </conditional>
             </conditional>
             <param name="include_gbff" value="true"/>
-            <param name="exclude_seq" value="false"/>
-            <param name="exclude_gff3" value="true"/>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="true"/>
+            <param name="exclude_genomic_cds" value="true"/>
             <param name="uncompressed" value="true"/>
             <param name="released_before" value="01/02/2007"></param>
             <output name="genome_data_report">
@@ -181,10 +208,6 @@
                    <has_text text="SAMN02604181"/>
                 </assert_contents>
             </output>
-            <output_collection name="sequence_report" type="list">
-                <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
-                <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
-            </output_collection>
             <output_collection name="genomic_gff" type="list">
                 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
                 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
@@ -194,6 +217,25 @@
                 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="accession"></param>
+                <conditional name="text_or_file">
+                    <param name="text_or_file" value="text"></param>
+                    <param name="accession" value="GCF_000001405.40"></param>
+                </conditional>
+            </conditional>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="true"/>
+            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_gff3" value="true"/>
+            <param name="uncompressed" value="true"/>
+            <param name="released_before" value="01/02/2007"></param>
+            <output_collection name="sequence_report">
+                <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
+            </output_collection>
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -203,11 +245,11 @@
 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
 
 Tthe default genome dataset includes the following files (if available):
+ * data_report.jsonl (genome assembly and annotation metadata, not always available)
  * genomic.fna (genomic sequences)
  * rna.fna (transcript sequences)
  * protein.faa (protein sequences)
  * genomic.gff (genome annotation in gff3 format)
- * data_report.jsonl (data report with genome assembly and annotation metadata)
  * dataset_catalog.json (a list of files and file types included in the dataset)
 ]]>
     </help>
--- a/macros.xml	Mon Mar 07 12:05:56 2022 +0000
+++ b/macros.xml	Wed May 04 13:15:43 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">13.4.0</token>
+    <token name="@TOOL_VERSION@">13.14.0</token>
     <token name="@PROFILE@">20.01</token>
     <token name="@LICENSE@">MIT</token>
     <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
@@ -68,18 +68,15 @@
         <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
         <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
     </xml>
-    <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file">
-        <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" />
-    </xml>
-    <xml name="anti-exclude" token_exclude_what="gff3" token_exclude_label="Include gff3 annotation file" token_checked="false">
-        <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" falsevalue="--exclude-@EXCLUDE_WHAT@" truevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
+    <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file" token_checked="false">
+        <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
     </xml>
     <xml name="excludes_genome">
-        <expand macro="anti-exclude" exclude_what="seq" exclude_label="Include genomic sequence file" checked="true"/>
-        <expand macro="anti-exclude" exclude_what="gff3" exclude_label="Include gff3 annotation file"/>
-        <expand macro="anti-exclude" exclude_what="genomic-cds" exclude_label="Include cds from genomic sequence file"/>
-        <expand macro="anti-exclude" exclude_what="protein" exclude_label="Include protein sequence file"/>
-        <expand macro="anti-exclude" exclude_what="rna" exclude_label="Include transcript sequence file"/>
+        <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
+        <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/>
+        <expand macro="exclude" exclude_what="genomic-cds" exclude_label="Exclude cds from genomic sequence file"/>
+        <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
+        <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
     </xml>
     <xml name="excludes_gene">
         <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GCF_000001405.40.seq.rpt.jsonl	Wed May 04 13:15:43 2022 +0000
@@ -0,0 +1,191 @@
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","gcCount":"103674491","genbankAccession":"CM000663.2","length":248956422,"refseqAccession":"NC_000001.11","role":"assembled-molecule","sortOrder":1,"ucscStyleName":"chr1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270706.1","length":175055,"refseqAccession":"NT_187361.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270706v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270707.1","length":32032,"refseqAccession":"NT_187362.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270707v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270708.1","length":127682,"refseqAccession":"NT_187363.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270708v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270709.1","length":66860,"refseqAccession":"NT_187364.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270709v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270710.1","length":40176,"refseqAccession":"NT_187365.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270710v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270711.1","length":42210,"refseqAccession":"NT_187366.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270711v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270712.1","length":176043,"refseqAccession":"NT_187367.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270712v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270713.1","length":40745,"refseqAccession":"NT_187368.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270713v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270714.1","length":41717,"refseqAccession":"NT_187369.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270714v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"10","gcCount":"59342366","genbankAccession":"CM000672.2","length":133797422,"refseqAccession":"NC_000010.11","role":"assembled-molecule","sortOrder":10,"ucscStyleName":"chr10"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"11","gcCount":"70204082","genbankAccession":"CM000673.2","length":135086622,"refseqAccession":"NC_000011.10","role":"assembled-molecule","sortOrder":11,"ucscStyleName":"chr11"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"12","gcCount":"58038673","genbankAccession":"CM000674.2","length":133275309,"refseqAccession":"NC_000012.12","role":"assembled-molecule","sortOrder":12,"ucscStyleName":"chr12"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"13","gcCount":"38619357","genbankAccession":"CM000675.2","length":114364328,"refseqAccession":"NC_000013.11","role":"assembled-molecule","sortOrder":13,"ucscStyleName":"chr13"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","gcCount":"45815948","genbankAccession":"CM000676.2","length":107043718,"refseqAccession":"NC_000014.9","role":"assembled-molecule","sortOrder":14,"ucscStyleName":"chr14"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000009.2","length":201709,"refseqAccession":"NT_113796.3","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000009v2_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000194.1","length":191469,"refseqAccession":"NT_113888.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000194v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000225.1","length":211173,"refseqAccession":"NT_167219.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000225v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270722.1","length":194050,"refseqAccession":"NT_187377.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270722v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270723.1","length":38115,"refseqAccession":"NT_187378.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270723v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270724.1","length":39555,"refseqAccession":"NT_187379.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270724v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270725.1","length":172810,"refseqAccession":"NT_187380.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270725v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270726.1","length":43739,"refseqAccession":"NT_187381.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270726v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"15","gcCount":"46742416","genbankAccession":"CM000677.2","length":101991189,"refseqAccession":"NC_000015.10","role":"assembled-molecule","sortOrder":15,"ucscStyleName":"chr15"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"15","genbankAccession":"KI270727.1","length":448248,"refseqAccession":"NT_187382.1","role":"unlocalized-scaffold","sortOrder":15,"ucscStyleName":"chr15_KI270727v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"16","gcCount":"48251436","genbankAccession":"CM000678.2","length":90338345,"refseqAccession":"NC_000016.10","role":"assembled-molecule","sortOrder":16,"ucscStyleName":"chr16"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"16","genbankAccession":"KI270728.1","length":1872759,"refseqAccession":"NT_187383.1","role":"unlocalized-scaffold","sortOrder":16,"ucscStyleName":"chr16_KI270728v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","gcCount":"46714680","genbankAccession":"CM000679.2","length":83257441,"refseqAccession":"NC_000017.11","role":"assembled-molecule","sortOrder":17,"ucscStyleName":"chr17"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"GL000205.2","length":185591,"refseqAccession":"NT_113930.2","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_GL000205v2_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270729.1","length":280839,"refseqAccession":"NT_187384.1","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_KI270729v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270730.1","length":112551,"refseqAccession":"NT_187385.1","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_KI270730v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"18","gcCount":"40613699","genbankAccession":"CM000680.2","length":80373285,"refseqAccession":"NC_000018.10","role":"assembled-molecule","sortOrder":18,"ucscStyleName":"chr18"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"19","gcCount":"32693605","genbankAccession":"CM000681.2","length":58617616,"refseqAccession":"NC_000019.10","role":"assembled-molecule","sortOrder":19,"ucscStyleName":"chr19"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","gcCount":"101284083","genbankAccession":"CM000664.2","length":242193529,"refseqAccession":"NC_000002.12","role":"assembled-molecule","sortOrder":2,"ucscStyleName":"chr2"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270715.1","length":161471,"refseqAccession":"NT_187370.1","role":"unlocalized-scaffold","sortOrder":2,"ucscStyleName":"chr2_KI270715v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270716.1","length":153799,"refseqAccession":"NT_187371.1","role":"unlocalized-scaffold","sortOrder":2,"ucscStyleName":"chr2_KI270716v1_random"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"20","gcCount":"28406612","genbankAccession":"CM000682.2","length":64444167,"refseqAccession":"NC_000020.11","role":"assembled-molecule","sortOrder":20,"ucscStyleName":"chr20"}
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+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270424.1","length":2140,"refseqAccession":"NT_187414.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270424v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270425.1","length":1884,"refseqAccession":"NT_187418.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270425v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270429.1","length":1361,"refseqAccession":"NT_187419.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270429v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270435.1","length":92983,"refseqAccession":"NT_187424.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270435v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270438.1","length":112505,"refseqAccession":"NT_187425.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270438v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270442.1","length":392061,"refseqAccession":"NT_187420.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270442v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270448.1","length":7992,"refseqAccession":"NT_187495.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270448v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270465.1","length":1774,"refseqAccession":"NT_187422.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270465v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270466.1","length":1233,"refseqAccession":"NT_187421.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270466v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270467.1","length":3920,"refseqAccession":"NT_187423.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270467v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270468.1","length":4055,"refseqAccession":"NT_187426.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270468v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270507.1","length":5353,"refseqAccession":"NT_187437.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270507v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270508.1","length":1951,"refseqAccession":"NT_187430.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270508v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270509.1","length":2318,"refseqAccession":"NT_187428.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270509v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270510.1","length":2415,"refseqAccession":"NT_187427.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270510v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270511.1","length":8127,"refseqAccession":"NT_187435.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270511v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270512.1","length":22689,"refseqAccession":"NT_187432.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270512v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270515.1","length":6361,"refseqAccession":"NT_187436.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270515v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270516.1","length":1300,"refseqAccession":"NT_187431.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270516v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270517.1","length":3253,"refseqAccession":"NT_187438.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270517v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270518.1","length":2186,"refseqAccession":"NT_187429.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270518v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270519.1","length":138126,"refseqAccession":"NT_187433.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270519v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270521.1","length":7642,"refseqAccession":"NT_187496.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270521v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270522.1","length":5674,"refseqAccession":"NT_187434.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270522v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270528.1","length":2983,"refseqAccession":"NT_187440.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270528v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270529.1","length":1899,"refseqAccession":"NT_187439.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270529v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270530.1","length":2168,"refseqAccession":"NT_187441.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270530v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270538.1","length":91309,"refseqAccession":"NT_187443.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270538v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270539.1","length":993,"refseqAccession":"NT_187442.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270539v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270544.1","length":1202,"refseqAccession":"NT_187444.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270544v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270548.1","length":1599,"refseqAccession":"NT_187445.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270548v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270579.1","length":31033,"refseqAccession":"NT_187450.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270579v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270580.1","length":1553,"refseqAccession":"NT_187448.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270580v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270581.1","length":7046,"refseqAccession":"NT_187449.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270581v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270582.1","length":6504,"refseqAccession":"NT_187454.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270582v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270583.1","length":1400,"refseqAccession":"NT_187446.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270583v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270584.1","length":4513,"refseqAccession":"NT_187453.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270584v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270587.1","length":2969,"refseqAccession":"NT_187447.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270587v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270588.1","length":6158,"refseqAccession":"NT_187455.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270588v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270589.1","length":44474,"refseqAccession":"NT_187451.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270589v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270590.1","length":4685,"refseqAccession":"NT_187452.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270590v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270591.1","length":5796,"refseqAccession":"NT_187457.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270591v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270593.1","length":3041,"refseqAccession":"NT_187456.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270593v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270741.1","length":157432,"refseqAccession":"NT_187497.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270741v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270742.1","length":186739,"refseqAccession":"NT_187513.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270742v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270743.1","length":210658,"refseqAccession":"NT_187498.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270743v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270744.1","length":168472,"refseqAccession":"NT_187499.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270744v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270745.1","length":41891,"refseqAccession":"NT_187500.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270745v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270746.1","length":66486,"refseqAccession":"NT_187501.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270746v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270747.1","length":198735,"refseqAccession":"NT_187502.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270747v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270748.1","length":93321,"refseqAccession":"NT_187503.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270748v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270749.1","length":158759,"refseqAccession":"NT_187504.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270749v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270750.1","length":148850,"refseqAccession":"NT_187505.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270750v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270751.1","length":150742,"refseqAccession":"NT_187506.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270751v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270753.1","length":62944,"refseqAccession":"NT_187508.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270753v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270754.1","length":40191,"refseqAccession":"NT_187509.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270754v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270755.1","length":36723,"refseqAccession":"NT_187510.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270755v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270756.1","length":79590,"refseqAccession":"NT_187511.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270756v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270757.1","length":71251,"refseqAccession":"NT_187512.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270757v1"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"X","gcCount":"67807309","genbankAccession":"CM000685.2","length":156040895,"refseqAccession":"NC_000023.11","role":"assembled-molecule","sortOrder":23,"ucscStyleName":"chrX"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Y","gcCount":"10963787","genbankAccession":"CM000686.2","length":57227415,"refseqAccession":"NC_000024.10","role":"assembled-molecule","sortOrder":24,"ucscStyleName":"chrY"}
+{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Y","genbankAccession":"KI270740.1","length":37240,"refseqAccession":"NT_187395.1","role":"unlocalized-scaffold","sortOrder":24,"ucscStyleName":"chrY_KI270740v1_random"}
+{"assemblyUnit":"GCF_000006015.1","assignedMoleculeLocationType":"Mitochondrion","chrName":"MT","gcCount":"7350","genbankAccession":"J01415.2","length":16569,"refseqAccession":"NC_012920.1","role":"assembled-molecule","sortOrder":1,"ucscStyleName":"chrM"}
--- a/test-data/GCF_000007445.1.genomic.gtf	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/GCF_000007445.1.genomic.gtf	Wed May 04 13:15:43 2022 +0000
@@ -1,7 +1,3 @@
-#gtf-version 2.2
-#!genome-build ASM744v1
-#!genome-build-accession NCBI_Assembly:GCF_000007445.1
-#!annotation-date 05/06/2021 17:43:00
 #!annotation-source NCBI RefSeq 
 NC_004431.1	RefSeq	gene	190	255	.	+	.	gene_id "C_RS00005"; transcript_id ""; gbkey "Gene"; gene "thrL"; gene_biotype "protein_coding"; locus_tag "C_RS00005"; old_locus_tag "c5491"; 
 NC_004431.1	Protein Homology	CDS	190	252	.	+	0	gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "C_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11"; 
--- a/test-data/genome.2.GCF_000007445.1.seq.rpt.jsonl	Mon Mar 07 12:05:56 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1}
--- a/test-data/genome.2.GCF_000013305.1.genomic.gtf	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/genome.2.GCF_000013305.1.genomic.gtf	Wed May 04 13:15:43 2022 +0000
@@ -1,7 +1,3 @@
-#gtf-version 2.2
-#!genome-build ASM1330v1
-#!genome-build-accession NCBI_Assembly:GCF_000013305.1
-#!annotation-date 05/06/2021 17:31:48
 #!annotation-source NCBI RefSeq 
 NC_008253.1	RefSeq	gene	190	255	.	+	.	gene_id "ECP_RS00005"; transcript_id ""; gbkey "Gene"; gene "thrL"; gene_biotype "protein_coding"; locus_tag "ECP_RS00005"; old_locus_tag "ECP_0001"; 
 NC_008253.1	Protein Homology	CDS	190	252	.	+	0	gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_414542.1"; locus_tag "ECP_RS00005"; product "thr operon leader peptide"; protein_id "WP_001386572.1"; transl_table "11"; 
--- a/test-data/genome.2.GCF_000013305.1.seq.rpt.jsonl	Mon Mar 07 12:05:56 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1}
--- a/test-data/genome.3.GCF_000007445.1.genomic.gbff	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/genome.3.GCF_000007445.1.genomic.gbff	Wed May 04 13:15:43 2022 +0000
@@ -1,4 +1,3 @@
-LOCUS       NC_004431            5231428 bp    DNA     circular CON 13-MAY-2021
 DEFINITION  Escherichia coli CFT073, complete sequence.
 ACCESSION   NC_004431 NZ_AE016755 NZ_AE016756 NZ_AE016757 NZ_AE016758
             NZ_AE016759 NZ_AE016760 NZ_AE016761 NZ_AE016762 NZ_AE016763
--- a/test-data/genome.3.GCF_000007445.1.genomic.gff	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/genome.3.GCF_000007445.1.genomic.gff	Wed May 04 13:15:43 2022 +0000
@@ -1,10 +1,2 @@
-##gff-version 3
-#!gff-spec-version 1.21
-#!processor NCBI annotwriter
-#!genome-build ASM744v1
-#!genome-build-accession NCBI_Assembly:GCF_000007445.1
-#!annotation-date 05/06/2021 17:43:00
-#!annotation-source NCBI RefSeq 
-##sequence-region NC_004431.1 1 5231428
 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=199310
 NC_004431.1	RefSeq	region	1	5231428	.	+	.	ID=NC_004431.1:1..5231428;Dbxref=taxon:199310;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=CFT073
--- a/test-data/genome.3.GCF_000007445.1.seq.rpt.jsonl	Mon Mar 07 12:05:56 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"assemblyUnit":"GCF_000007455.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2640553","genbankAccession":"AE014075.1","length":5231428,"refseqAccession":"NC_004431.1","sortOrder":1}
--- a/test-data/genome.3.GCF_000013305.1.genomic.gbff	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/genome.3.GCF_000013305.1.genomic.gbff	Wed May 04 13:15:43 2022 +0000
@@ -1,4 +1,3 @@
-LOCUS       NC_008253            4938920 bp    DNA     circular CON 13-MAY-2021
 DEFINITION  Escherichia coli 536, complete sequence.
 ACCESSION   NC_008253
 VERSION     NC_008253.1
--- a/test-data/genome.3.GCF_000013305.1.genomic.gff	Mon Mar 07 12:05:56 2022 +0000
+++ b/test-data/genome.3.GCF_000013305.1.genomic.gff	Wed May 04 13:15:43 2022 +0000
@@ -1,10 +1,2 @@
-##gff-version 3
-#!gff-spec-version 1.21
-#!processor NCBI annotwriter
-#!genome-build ASM1330v1
-#!genome-build-accession NCBI_Assembly:GCF_000013305.1
-#!annotation-date 05/06/2021 17:31:48
-#!annotation-source NCBI RefSeq 
-##sequence-region NC_008253.1 1 4938920
 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=362663
 NC_008253.1	RefSeq	region	1	4938920	.	+	.	ID=NC_008253.1:1..4938920;Dbxref=taxon:362663;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;serogroup=O6:K15:H31;strain=536
--- a/test-data/genome.3.GCF_000013305.1.seq.rpt.jsonl	Mon Mar 07 12:05:56 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"assemblyUnit":"GCF_000013315.1","assignedMoleculeLocationType":"Chromosome","chrName":"ANONYMOUS","gcCount":"2495020","genbankAccession":"CP000247.1","length":4938920,"refseqAccession":"NC_008253.1","sortOrder":1}