Repository 'ncbi_datasets'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets

Changeset 21:0f3b3813b6ae (2025-07-21)
Previous changeset 20:7b925f7c50b2 (2025-03-17) Next changeset 22:03a801ded645 (2025-07-29)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c1c3f90e4aa7dc258aa61d98ec4eac0b97eef426
modified:
datasets_gene.xml
datasets_genome.xml
macros.xml
test-data/GCF_000007445.1.genomic.gtf
test-data/genome.2.GCF_000013305.1.genomic.gtf
b
diff -r 7b925f7c50b2 -r 0f3b3813b6ae datasets_gene.xml
--- a/datasets_gene.xml Mon Mar 17 11:05:45 2025 +0000
+++ b/datasets_gene.xml Mon Jul 21 19:28:16 2025 +0000
[
b'@@ -4,7 +4,7 @@\n         <import>macros.xml</import>\n     </macros>\n     <expand macro="bio_tools"/>\n-    <expand macro="requirements"></expand>\n+    <expand macro="requirements"/>\n     <expand macro="version_command"/>\n     <command><![CDATA[\n #import re\n@@ -41,7 +41,7 @@\n \n #if $filters.fasta_filter_cond.fasta_filter_select\n     #if $filters.fasta_filter_cond.fasta_filter_select == \'text\'\n-        --fasta-filter #echo ",".join(f"\'{x}\'" for x in $filters.fasta_filter_cond.fasta_filter.split(\',\') if x)\n+        --fasta-filter #echo ",".join(f"\'{x}\'" for x in str($filters.fasta_filter_cond.fasta_filter).split(\',\') if x)\n     #else\n         --fasta-filter-file \'$filters.fasta_filter_cond.fasta_filter_file\'\n     #end if\n@@ -97,8 +97,8 @@\n                     <param argument="--taxon" type="text" value="human" label="Species for gene symbol" help="NCBI taxid, common or scientific name">\n                         <sanitizer invalid_char="">\n                             <valid initial="string.letters">\n-                                <add value=" " />\n-                                <add value="-" />\n+                                <add value=" "/>\n+                                <add value="-"/>\n                             </valid>\n                         </sanitizer>\n                     </param>\n@@ -109,8 +109,8 @@\n                     <param argument="--taxon-filter" type="text" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions">\n                         <sanitizer invalid_char="">\n                             <valid initial="string.letters">\n-                                <add value=" " />\n-                                <add value="-" />\n+                                <add value=" "/>\n+                                <add value="-"/>\n                             </valid>\n                         </sanitizer>\n                     </param>\n@@ -133,7 +133,7 @@\n                     <param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated">\n                         <sanitizer invalid_char="">\n                             <valid initial="string.letters,string.digits">\n-                                <add value="," />\n+                                <add value=","/>\n                             </valid>\n                         </sanitizer>\n                     </param>\n@@ -235,12 +235,12 @@\n             </output>\n             <output name="rna_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n             <output name="protein_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n         </test>\n@@ -263,12 +263,12 @@\n             </output>\n             <output name="rna_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n             <output name="protein_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n         </test>\n@@ -284,6 +284,7 @@\n             </conditional>\n             <section name="file_choices">\n                 <conditional name="kingdom_cond">\n+                    <param name="kingdom_sel" value="gene"/>\n                     <param name="include" value="gene,cds"/>\n                 </conditional>\n             </section>\n@@ -297,17 +298,17 @@\n             </output>\n             <output name="gene_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n'..b'fivep_utr_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n         </test>\n         <!-- 6: datasets download gene symbol brca1 \\-\\-ortholog -->\n-        <test expect_num_outputs="1">\n+        <test expect_num_outputs="3">\n             <conditional name="query|subcommand">\n                 <param name="download_by" value="symbol"/>\n                 <conditional name="text_or_file">\n@@ -380,11 +376,6 @@\n                 </conditional>\n                 <param name="ortholog" value="rodentia"/>\n             </conditional>\n-            <section name="file_choices">\n-                <conditional name="kingdom_cond">\n-                    <param name="include" value=""/>\n-                </conditional>\n-            </section>\n             <output name="gene_data_report">\n                 <assert_contents>\n                     <has_text text="rat"/>\n@@ -395,7 +386,7 @@\n             </output>\n         </test>\n         <!-- 7: datasets download gene accession NP_000483.3 -->\n-        <test expect_num_outputs="1">\n+        <test expect_num_outputs="3">\n             <conditional name="query|subcommand">\n                 <param name="download_by" value="accession"/>\n                 <conditional name="text_or_file">\n@@ -403,11 +394,6 @@\n                     <param name="accession" value="NP_000483.3"/>\n                 </conditional>\n             </conditional>\n-            <section name="file_choices">\n-                <conditional name="kingdom_cond">\n-                    <param name="include" value=""/>\n-                </conditional>\n-            </section>\n             <output name="gene_data_report">\n                 <assert_contents>\n                     <has_text text="human"/>\n@@ -417,7 +403,7 @@\n             </output>\n         </test>\n         <!-- 8: datasets download gene accession NM_000546.6 NM_000492.4 + ortholog-->\n-        <test expect_num_outputs="1">\n+        <test expect_num_outputs="3">\n             <conditional name="query|subcommand">\n                 <param name="download_by" value="accession"/>\n                 <conditional name="text_or_file">\n@@ -426,11 +412,6 @@\n                 </conditional>\n                 <param name="ortholog" value="all"/>\n             </conditional>\n-            <section name="file_choices">\n-                <conditional name="kingdom_cond">\n-                    <param name="include" value=""/>\n-                </conditional>\n-            </section>\n             <output name="gene_data_report">\n                 <assert_contents>\n                     <has_text text="human"/>\n@@ -439,7 +420,6 @@\n                 </assert_contents>\n             </output>\n         </test>\n-\n         <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp -->\n         <test expect_num_outputs="4">\n             <conditional name="query|subcommand">\n@@ -466,24 +446,23 @@\n             </output>\n             <output name="gene_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n             <output name="gene_flanks">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n             <output name="protein_fasta">\n                 <assert_contents>\n-                    <has_text text=">"/>\n+                    <has_text text="&gt;"/>\n                 </assert_contents>\n             </output>\n             <assert_command>\n                 <has_text text="include-flanks-bp 100"/>\n             </assert_command>\n-        </test> \n-\n+        </test>\n         <!-- 10: datasets download gene taxon human   -->\n         <!-- <test expect_num_outputs="1">\n             <conditional name="query|subcommand">\n'
b
diff -r 7b925f7c50b2 -r 0f3b3813b6ae datasets_genome.xml
--- a/datasets_genome.xml Mon Mar 17 11:05:45 2025 +0000
+++ b/datasets_genome.xml Mon Jul 21 19:28:16 2025 +0000
[
b'@@ -4,9 +4,14 @@\n         <import>macros.xml</import>\n     </macros>\n     <expand macro="bio_tools"/>\n-    <expand macro="requirements"></expand>\n+    <expand macro="requirements"/>\n     <expand macro="version_command"/>\n-    <command><![CDATA[\n+    <stdio>\n+        <regex match="Warning" source="stderr" level="warning" description=""/>\n+        <regex match="skipping" source="stderr" level="warning" description=""/>\n+        <regex match="ERROR" level="fatal"/>\n+    </stdio>\n+    <command detect_errors="exit_code"><![CDATA[\n #import re\n @SETUP_CERTIFICATES@\n datasets download genome $query.subcommand.download_by\n@@ -116,7 +121,6 @@\n             </param>\n             <expand macro="released_options"/>\n             <expand macro="released_options" before_or_after="after"/>\n-\n             <repeat name="search" title="Add search terms">\n                 <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"/>\n             </repeat>\n@@ -137,35 +141,35 @@\n     <outputs>\n         <data name="genome_data_report" format="tabular" label="NCBI Genome Datasets: Data Report" from_work_dir="genome_data_report.tsv"/>\n         <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">\n-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/sequence_report.tsv" ext="tabular" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>\n+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/sequence_report.tsv" ext="tabular" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>\n             <filter>file_choices[\'include\'] and "seq-report" in file_choices[\'include\']</filter>\n         </collection>\n         <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">\n-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?\\.(?P&lt;ext&gt;fasta(\\.gz)?)"  directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>\n+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?\\.(?P&lt;ext&gt;fasta(\\.gz)?)" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>\n             <filter>file_choices[\'include\'] and "genome" in file_choices[\'include\']</filter>\n         </collection>\n         <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">\n-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/rna\\.(?P&lt;ext&gt;fasta(\\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>\n+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/rna\\.(?P&lt;ext&gt;fasta(\\.gz)?)$" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>\n             <filter>file_choices[\'include\'] and "rna" in file_choices[\'include\']</filter>\n         </collection>\n         <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">\n-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/protein\\.(?P&lt;ext&gt;fasta(\\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>\n+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/protein\\.(?P&lt;ext&gt;fasta(\\.gz)?)$" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>\n             <filter>file_choices[\'include\'] and "protein" in file_choices[\'include\']</filter>\n         </collection>\n         <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">\n-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\\/cds_from_genomic\\.(?P&lt;ext&gt;fasta(\\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>\n+            <discover'..b'ame="released_before" value="01/01/2015"/>\n+                <param name="assembly_version" value="all"/>\n+            </section>\n             <section name="file_choices">\n                 <param name="include" value="seq-report"/>\n             </section>\n@@ -395,19 +409,19 @@\n                 <param name="decompress" value="true"/>\n             </section>\n             <output_collection name="genome_fasta" type="list:list" count="1">\n-                <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>\n+                <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression="&gt;NC_[0-9]+\\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>\n             </output_collection>\n             <output_collection name="protein_fasta" type="list" count="1">\n                 <element name="GCF_000146045.2" decompress="true">\n                     <assert_contents>\n-                        <has_text text=">"/>\n+                        <has_text text="&gt;"/>\n                     </assert_contents>\n                 </element>\n             </output_collection>\n             <output_collection name="rna_fasta" type="list" count="1">\n                 <element name="GCF_000146045.2" decompress="true">\n                     <assert_contents>\n-                        <has_text text=">"/>\n+                        <has_text text="&gt;"/>\n                     </assert_contents>\n                 </element>\n             </output_collection>\n@@ -437,7 +451,7 @@\n             <output_collection name="protein_fasta" type="list" count="1">\n                 <element name="GCF_000146045.2" ftype="fasta.gz">\n                     <assert_contents>\n-                        <has_size value="1845038" delta="2000"/>\n+                        <has_size value="1847862" delta="2000"/>\n                     </assert_contents>\n                 </element>\n             </output_collection>\n@@ -463,22 +477,21 @@\n             </section>\n             <output_collection name="sequence_report" type="list" count="2"/>\n             <output_collection name="genome_fasta" type="list:list" count="2">\n-                <expand macro="genome_fasta_assert" el1="GCF_000002945.2" el2="GCF_000002945.2_ASM294v3" expression=">NC_[0-9]+\\.[0-9]+ Schizosaccharomyces pombe.*" expression_n="4"/>\n-                <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\\.[0-9]+ Saccharomyces cerevisiae S288[Cc].*" expression_n="17"/>\n+                <expand macro="genome_fasta_assert" el1="GCF_000002945.2" el2="GCF_000002945.2_ASM294v3" expression="&gt;NC_[0-9]+\\.[0-9]+ Schizosaccharomyces pombe.*" expression_n="4"/>\n+                <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression="&gt;NC_[0-9]+\\.[0-9]+ Saccharomyces cerevisiae S288[Cc].*" expression_n="17"/>\n             </output_collection>\n         </test>\n         <!-- tax_exact_match should filter out strains\n              https://github.com/ncbi/datasets/issues/187 -->\n-        <test expect_num_outputs="1">\n+        <test expect_num_outputs="2">\n             <conditional name="query|subcommand">\n                 <param name="download_by" value="taxon"/>\n                 <param name="taxon_positional" value="4932"/>\n                 <param name="tax_exact_match" value="true"/>\n             </conditional>\n-            <param name="include" value=""/>\n             <output name="genome_data_report">\n                 <assert_contents>\n-                   <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>\n+                    <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>\n                 </assert_contents>\n             </output>\n         </test>\n'
b
diff -r 7b925f7c50b2 -r 0f3b3813b6ae macros.xml
--- a/macros.xml Mon Mar 17 11:05:45 2025 +0000
+++ b/macros.xml Mon Jul 21 19:28:16 2025 +0000
[
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">17.1.0</token>
+    <token name="@TOOL_VERSION@">18.4.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.0</token>
     <token name="@LICENSE@">MIT</token>
@@ -12,7 +12,8 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
             <requirement type="package" version="2025.1.31">ca-certificates</requirement>
-            <requirement type="package" version="6.0">unzip</requirement>
+             <!-- Removed line below because it was causing "skipping: [..] need PK compat. v4.5 (can do v2.1)"  -->
+             <!-- <requirement type="package" version="6.0">unzip</requirement> -->
         </requirements>
     </xml>
     <xml name="bio_tools">
b
diff -r 7b925f7c50b2 -r 0f3b3813b6ae test-data/GCF_000007445.1.genomic.gtf
--- a/test-data/GCF_000007445.1.genomic.gtf Mon Mar 17 11:05:45 2025 +0000
+++ b/test-data/GCF_000007445.1.genomic.gtf Mon Jul 21 19:28:16 2025 +0000
b
@@ -1,6 +1,5 @@
-#!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"; 
-NC_004431.1 Protein Homology start_codon 190 192 . + 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"; 
-NC_004431.1 Protein Homology stop_codon 253 255 . + 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"; 
+NC_004431.1 Protein Homology CDS 190 252 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
+NC_004431.1 Protein Homology start_codon 190 192 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
+NC_004431.1 Protein Homology stop_codon 253 255 . + 0 gene_id "C_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
 NC_004431.1 RefSeq gene 453 911 . + . gene_id "C_RS00010"; transcript_id ""; gbkey "Gene"; gene "tnpA"; gene_biotype "protein_coding"; locus_tag "C_RS00010"; old_locus_tag "c0002"; 
b
diff -r 7b925f7c50b2 -r 0f3b3813b6ae test-data/genome.2.GCF_000013305.1.genomic.gtf
--- a/test-data/genome.2.GCF_000013305.1.genomic.gtf Mon Mar 17 11:05:45 2025 +0000
+++ b/test-data/genome.2.GCF_000013305.1.genomic.gtf Mon Jul 21 19:28:16 2025 +0000
b
@@ -1,6 +1,5 @@
-#!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"; 
-NC_008253.1 Protein Homology start_codon 190 192 . + 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"; 
-NC_008253.1 Protein Homology stop_codon 253 255 . + 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"; 
+NC_008253.1 Protein Homology CDS 190 252 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
+NC_008253.1 Protein Homology start_codon 190 192 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
+NC_008253.1 Protein Homology stop_codon 253 255 . + 0 gene_id "ECP_RS00005"; transcript_id "unassigned_transcript_1"; db_xref "GenBank:WP_001386572.1"; 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"; exon_number "1"; 
 NC_008253.1 RefSeq gene 336 2798 . + . gene_id "ECP_RS00010"; transcript_id ""; gbkey "Gene"; gene "thrA"; gene_biotype "protein_coding"; locus_tag "ECP_RS00010"; old_locus_tag "ECP_0002";