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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f |
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modified:
get_organelle_from_reads.xml |
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added:
get_annotated_regions_from_gb.xml macros.xml test-data/NC_047059.gb test-data/NC_047060.gb test-data/NC_047400.gb |
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| diff -r 8b330a577046 -r 06bcf65179fb get_annotated_regions_from_gb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_annotated_regions_from_gb.xml Thu Feb 23 17:06:37 2023 +0000 |
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| @@ -0,0 +1,140 @@ +<tool id="get_annotated_regions_from_gb" name="Get annotated regions from genbank files (getorganelle)" version="0.1.0" python_template_version="3.5"> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">getorganelle</requirement> + <requirement type="package" version="@BIOPYTHON_VERSION@">biopython</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import re + + ## create list of symbolic links to input files + + #set file_names = [] + #for $input in $inputs + #set $input_name = re.sub('[^\w\-\s]', '_', str($input.name)).replace('_gb', '.gb') + ln -s '$input' '$input_name' && + $file_names.append($input_name) + #end for + + ## run python script + + get_annotated_regions_from_gb.py + #for file in file_names: + '$file' + #end for + -o results_directory + #if str($gene_type_selector) == "CDS": + -t CDS + #end if + #if str($gene_type_selector) == "tRNA": + -t tRNA + #end if + #if str($gene_type_selector) == "rRNA": + -t rRNA + #end if + --mix + + ]]></command> + <inputs> + <param type="data" multiple="true" name="inputs" format="gb" label="Annotated genbank file(s)" help="Genbank files with annotated regions to extract. Multiple files can be selected." /> + <param name="gene_type_selector" type="select" label="Gene type"> + <option value="CDS" selected="true">CDS</option> + <option value="tRNA">tRNA</option> + <option value="rRNA">rRNA</option> + </param> + </inputs> + <outputs> + <data name="output_fasta" format="fasta" from_work_dir="results_directory/gene/gene.fasta" label='${tool.name} on ${on_string}: Annotated genes'/> + </outputs> + <tests> + <test> + <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/> + <param name="gene_type_selector" value="CDS"/> + <assert_stdout> + <has_text text="Time cost" /> + </assert_stdout> + <output name="output_fasta"> + <assert_contents> + <has_line line=">matK CDS - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" /> + <has_line line=">matK CDS - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" /> + <has_line line=">matK CDS - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/> + <param name="gene_type_selector" value="tRNA"/> + <assert_stdout> + <has_text text="Time cost" /> + </assert_stdout> + <output name="output_fasta"> + <assert_contents> + <has_line line=">trnA-UGC tRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" /> + <has_line line=">trnA-UGC tRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" /> + <has_line line=">trnA-UGC tRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/> + <param name="gene_type_selector" value="rRNA"/> + <assert_stdout> + <has_text text="Time cost" /> + </assert_stdout> + <output name="output_fasta"> + <assert_contents> + <has_line line=">rrn16 rRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" /> + <has_line line=">rrn16 rRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" /> + <has_line line=">rrn16 rRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + + Python script to extract annotated genes from genbank files. The annotated genes are in the correct format to be used as seed sequences in GetOrganelle. + Help information from the python script is below. Only options for input genebank files and gene type are included in this tool. + + By jinjianjun@mail.kib.ac.cn 2017 + Usage: get_annotated_regions_from_gb.py gb_files -o out_dir + + Options: + -h, --help show this help message and exit + -o OUT_PUT Output. + -t GENE_TYPES Annotation type taken as gene. Default: CDS,tRNA,rRNA + --separate-copy By default, only keep one copy (see '--copy-mode' for + more) if there are several regions with the same name. + Exception: if there are one copy with intron(s) and + another copy without intron, they would be both kept. + This exception was specially made for the convenience + of commonly-incorrectly-annotated rps12 gene of + plastome. + --copy-mode=COPY_MODE + first|longest|leastN|leastN_longest (default). + --separate-exon By default, combining exons. + --keys=GENE_KEYS The key to the gene name: gene, label, product or + other keys in the qualifiers region.Default: + gene,label,product,note. + --mix Mix different genes into a single fasta file. In this + mode, the sequence header will be gene_name - gb_info + --case-mode=CASE_TREATMENT + first: Gene name case-non-sensitive. Consistent to the + first appearance. lower: Gene name case-non- + sensitive. All gene name set to lower case. upper: + Gene name case-non-sensitive. All gene name set to + Upper case. raw: Gene name case-sensitive. + --ignore-format-error + Skip the Error: key "*" not found in annotation. Not + suggested. + --translate-to-product + Translate the tRNA gene name to the form of their + product. Default: False + --overwrite Choose to overwrite previous result. + + ]]></help> + <citations> + <citation type="doi">10.1093/sysbio/syaa047</citation> + </citations> +</tool> |
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| diff -r 8b330a577046 -r 06bcf65179fb get_organelle_from_reads.xml --- a/get_organelle_from_reads.xml Wed Sep 28 22:05:41 2022 +0000 +++ b/get_organelle_from_reads.xml Thu Feb 23 17:06:37 2023 +0000 |
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| @@ -1,6 +1,6 @@ <tool id="get_organelle_from_reads" name="Get organelle from reads" version="@TOOL_VERSION@"> <macros> - <token name="@TOOL_VERSION@">1.7.6.1</token> + <import>macros.xml</import> <xml name="seed_and_genes" tokens="optional"> <param type="data" argument="-s" format="fasta" optional="@OPTIONAL@" label="Seed sequence(s)" help="Fasta file to use as initial seed. A seed sequence in GetOrganelle is only used for identifying initial organelle reads."/> <param type="data" argument="--genes" format="fasta" optional="@OPTIONAL@" label="Gene sequence(s)" help="Fasta file containing protein coding genes and ribosomal RNAs extracted from a reference genome that you want to assemble."/> |
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| diff -r 8b330a577046 -r 06bcf65179fb macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 23 17:06:37 2023 +0000 |
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| @@ -0,0 +1,4 @@ +<macros> + <token name="@TOOL_VERSION@">1.7.7.0</token> + <token name="@BIOPYTHON_VERSION@">1.79</token> +</macros> |
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| diff -r 8b330a577046 -r 06bcf65179fb test-data/NC_047059.gb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_047059.gb Thu Feb 23 17:06:37 2023 +0000 |
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| b'@@ -0,0 +1,4672 @@\n+LOCUS NC_047059 158656 bp DNA circular PLN 17-APR-2020\n+DEFINITION Styphnolobium japonicum voucher Yi15212-KUN plastid, complete\n+ genome.\n+ACCESSION NC_047059\n+VERSION NC_047059.1\n+DBLINK BioProject: PRJNA626053\n+KEYWORDS RefSeq.\n+SOURCE plastid Styphnolobium japonicum (Japanese pagoda tree)\n+ ORGANISM Styphnolobium japonicum\n+ Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n+ Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;\n+ Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae;\n+ Cladrastis clade; Styphnolobium.\n+REFERENCE 1 (bases 1 to 158656)\n+ AUTHORS Zhang,R., Wang,Y.H., Jin,J.J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.D., Chen,S.Y., Wang,J., Li,D.Z.\n+ and Yi,T.S.\n+ TITLE Exploration of Plastid Phylogenomic Conflict Yields New Insights\n+ into the Deep Relationships of Leguminosae\n+ JOURNAL Syst. Biol. (2020) In press\n+ PUBMED 32065640\n+ REMARK Publication Status: Available-Online prior to print\n+REFERENCE 2 (bases 1 to 158656)\n+ CONSRTM NCBI Genome Project\n+ TITLE Direct Submission\n+ JOURNAL Submitted (17-APR-2020) National Center for Biotechnology\n+ Information, NIH, Bethesda, MD 20894, USA\n+REFERENCE 3 (bases 1 to 158656)\n+ AUTHORS Zhang,R., Wang,Y.-H., Jin,J.-J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.-D., Chen,S.-Y., Wang,J.,\n+ Li,D.-Z. and Yi,T.-S.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (18-NOV-2019) Germplasm Bank of Wild Species, Kunming\n+ Institute of Botany, 132 Lanhei Rd, Kunming, Yunnan 650201, China\n+COMMENT ##Assembly-Data-START##\n+ Assembly Method :: GetOrganelle v. August 25, 2016; CLC\n+ Sequencing Technology :: Illumina\n+ ##Assembly-Data-END##\n+ PROVISIONAL REFSEQ: This record has not yet been subject to final\n+ NCBI review. The reference sequence is identical to MN709788.\n+ Genomics Workbench v. v8.5.1\n+ COMPLETENESS: full length.\n+FEATURES Location/Qualifiers\n+ source 1..158656\n+ /organism="Styphnolobium japonicum"\n+ /organelle="plastid"\n+ /mol_type="genomic DNA"\n+ /specimen_voucher="Yi15212-KUN"\n+ /db_xref="taxon:3897"\n+ /tissue_type="Fresh"\n+ gene complement(join(102600..103393,73767..73880))\n+ /gene="rps12"\n+ /locus_tag="HHI28_pgp041"\n+ /trans_splicing=""\n+ /db_xref="GeneID:54371971"\n+ CDS complement(join(102600..102625,103162..103393,\n+ 73767..73880))\n+ /gene="rps12"\n+ /locus_tag="HHI28_pgp041"\n+ /trans_splicing=""\n+ /codon_start=1\n+ /transl_table=11\n+ /product="ribosomal protein S12"\n+ /protein_id="YP_009755925.1"\n+ /db_xref="GeneID:54371971"\n+ /translation="MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKP\n+ NSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDA\n+ VGVKDRQQGRSKYGVKKPK"\n+ gene complement(45..118)\n+ /gene="trnH-GUG"\n+ /locus_tag="HHI28_pgt001"\n+ /db_xref="GeneID:54371842"\n+ tRNA complement(45..118)\n+ /gene="trnH-GUG"\n+ /locus_tag="HHI28_pgt001"\n+ /product="tRNA-His"\n+ /note="anticodon:GUG"\n+ /db_xref="GeneID:54371842"\n+ gene complement(515..1576)\n+'..b'aagag atgggaaaca tgctcaatat catttgattg\n+ 155581 aatagttgac ccagcccctt gttgtttgaa gaaaccctcc acttcaattg gtattttttc\n+ 155641 gcgaaaagca aacatgagat aataaatcca gtctttcact aagatttcga atagctgtcc\n+ 155701 cgaattcaag ttgattatgt ttcgcctctt cctcggagaa agacgatcaa acaattccca\n+ 155761 atcatggtcc ttgcggatcg gatcatccat ataatataca aaaagaaact ccagatattt\n+ 155821 gatatctttc tctttgaatg agatctcaat tccagcgacg gtttcattag atatcttaca\n+ 155881 actagaatcc ctcttttttc cgatccagtt cctccaccac cgcgaacccc agttagattc\n+ 155941 aggcatgata cactttttag ttattgggag aacccaagta ctctctttcg gatccaggaa\n+ 156001 agagctctca gagatctttt ttccttttgg aagatacagg agcgaaacaa tcaaccaatt\n+ 156061 gatattggaa gactcaaaag attcttccaa tgtatcattt ctgggtccaa tggaattcat\n+ 156121 aggtatagga agaagccctg tcaaatagag attttttctt tcgaccatct ttcgattgtt\n+ 156181 aatacgatat ataaggaccg ctactacaaa gagtactaca cccttgatcg tgaaatatcg\n+ 156241 attgcttgtt gaaccctgtg aattgcgtga aagtaggata ctccaaattc gggagtccaa\n+ 156301 gagttttata aaacgctctt gatggaaaaa aatgtgaatg aaagatccca ctgaattgaa\n+ 156361 ttgggtccat gaatctaaga aatagtgaga attcttgatc tctctcaata tctctctcaa\n+ 156421 ttcgaaaatc caggatttga attgatgtcc tttcattgaa tcctcctaaa ttgcattgat\n+ 156481 ttatcctaaa gatttcattt caattggaat ttggttattc accatgtacg aggatccccg\n+ 156541 ctaagcatcc atggctgaat ggttaaagcg cccaactcat aattggcgaa ttcgtaggtt\n+ 156601 caattcctac tggatgcacg ccaatgggac cctccaataa gtctattgga attggctctg\n+ 156661 tatcaatgga atctcatcat ccatccataa cgaattggtg tggtatattc atatcataac\n+ 156721 atatgaacag taagaactag cattcttatt gagactagaa ctcataggga agaaaataga\n+ 156781 tttatggatg gaatcaaata tgcagtattt acagacaaaa gtattcggtt attggggaaa\n+ 156841 aatcaatata cttctaatgt cgaatcagga tcaactagga cagaaataaa gcattgggtc\n+ 156901 gaactcttct ttggtgtcaa ggtaatagct atgaatagtc atcgactccc ggtaaagggt\n+ 156961 agaagaatgg gacctattat gggacataca atgcattaca gacgtatgat cattacgctt\n+ 157021 caaccgggtt attctattcc acctcttaga aagaaaagaa cttaaatcaa aatacttaat\n+ 157081 agcatggcga tacatttata caaaacttct accccgagca cacgcaatgg agccgtagac\n+ 157141 agtcaagtga aatccaatcc acgaaataat ttgatctatg gacagcatcg ttgtggtaaa\n+ 157201 ggccgtaatg ccagaggaat cattaccgca gggcatagag ggggaggtca taagcgttta\n+ 157261 taccgtaaaa tcgattttcg acggaatgaa aaagacatat atggtagaat cataaccata\n+ 157321 gaatacgacc ctaatcgaaa tgcatacatt tgtctcatac actatgggga tggtgagaaa\n+ 157381 agatatattt tacatcccag aggggctata attggagata ccattgtttc tggtacagaa\n+ 157441 gttcctataa aaatgggaaa tgccctacct ttgagtgcgg tttgaactat tgatttacgt\n+ 157501 aattggaagt aaccaattag gtttacggcg aaacctagaa atcgatcact gatccaattt\n+ 157561 gagtacctct acaggataga cctcaacaga aaactgaaga gtaacggcag caagtgattg\n+ 157621 agttcagtag ttcctcatat aaaattattg actctagaga tatagtaata tggagaagac\n+ 157681 aaaattgttt caagcaccga cagaaccaga agcgcccctt gtttcaaaga ggggaggacg\n+ 157741 ggttattcac atttcatttg atggtcagag gcgaattgaa agctaagcag tggtaattct\n+ 157801 aaggattccc cgggggaaaa atagagatgt ctcctacgtt acccgtacta tgtggaagta\n+ 157861 gcgacgtaat ttcatagagt cattcggtct gaatgctaca tgaagaacat aagccagatg\n+ 157921 aaggaacggg aagacctagg atgtagaaga tcataacatg agtgattcgg cagatttgga\n+ 157981 ttcctatata tccactcatg cggtacttca ttgtgcgata tatataagaa ttctacgata\n+ 158041 tatataagat ccatctgtat agatatcatc atctacatcc ggaaagccgt atgctttgga\n+ 158101 agaagcttgt acagtttggg aaggggtttt gattgatcaa aaagaagaat ctacttcaac\n+ 158161 cgatatgccc ttaggcacgg ccatacataa catagaaatc acactcggaa agggtggaca\n+ 158221 attagctaga gcagcaggtg ctgtagcgaa actgattgca aaagagggga aatcggccac\n+ 158281 attaaaatta ccttctgggg aggtccgttt gatatccaaa aactgctcag caacagtcgg\n+ 158341 acaagtgggg aatgttgggg taaaccagaa aagtttgggt agagccggat cgaaatgttg\n+ 158401 gctaggtaag cgtcctgtag taagaggagt agttatgaac cctgtagacc atccccatgg\n+ 158461 gggtggtgaa gggagggccc caattggtag aaaaaaaccc gcaactcctt ggggttatcc\n+ 158521 tgcacttgga agaagaagta gaaaaaggaa taaatatagt gataatttga ttcttcgtcg\n+ 158581 ccgtagtaaa tagtagagta gagaaaatag aatttgtttc ttcgtcttta caaaaaaaaa\n+ 158641 taggagtaat taactg\n+//\n' |
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| diff -r 8b330a577046 -r 06bcf65179fb test-data/NC_047060.gb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_047060.gb Thu Feb 23 17:06:37 2023 +0000 |
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| b'@@ -0,0 +1,4599 @@\n+LOCUS NC_047060 157616 bp DNA circular PLN 17-APR-2020\n+DEFINITION Haematoxylum brasiletto voucher N._Zamora6857-Costa_Rica plastid,\n+ complete genome.\n+ACCESSION NC_047060\n+VERSION NC_047060.1\n+DBLINK BioProject: PRJNA626055\n+KEYWORDS RefSeq.\n+SOURCE plastid Haematoxylum brasiletto\n+ ORGANISM Haematoxylum brasiletto\n+ Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n+ Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;\n+ Pentapetalae; rosids; fabids; Fabales; Fabaceae; Caesalpinioideae;\n+ Cassia clade; Haematoxylum.\n+REFERENCE 1 (bases 1 to 157616)\n+ AUTHORS Zhang,R., Wang,Y.H., Jin,J.J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.D., Chen,S.Y., Wang,J., Li,D.Z.\n+ and Yi,T.S.\n+ TITLE Exploration of Plastid Phylogenomic Conflict Yields New Insights\n+ into the Deep Relationships of Leguminosae\n+ JOURNAL Syst. Biol. (2020) In press\n+ PUBMED 32065640\n+ REMARK Publication Status: Available-Online prior to print\n+REFERENCE 2 (bases 1 to 157616)\n+ CONSRTM NCBI Genome Project\n+ TITLE Direct Submission\n+ JOURNAL Submitted (17-APR-2020) National Center for Biotechnology\n+ Information, NIH, Bethesda, MD 20894, USA\n+REFERENCE 3 (bases 1 to 157616)\n+ AUTHORS Zhang,R., Wang,Y.-H., Jin,J.-J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.-D., Chen,S.-Y., Wang,J.,\n+ Li,D.-Z. and Yi,T.-S.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (18-NOV-2019) Germplasm Bank of Wild Species, Kunming\n+ Institute of Botany, 132 Lanhei Rd, Kunming, Yunnan 650201, China\n+COMMENT ##Assembly-Data-START##\n+ Assembly Method :: GetOrganelle v. August 25, 2016; CLC\n+ Sequencing Technology :: Illumina\n+ ##Assembly-Data-END##\n+ PROVISIONAL REFSEQ: This record has not yet been subject to final\n+ NCBI review. The reference sequence is identical to MN709823.\n+ Genomics Workbench v. v8.5.1\n+ COMPLETENESS: full length.\n+FEATURES Location/Qualifiers\n+ source 1..157616\n+ /organism="Haematoxylum brasiletto"\n+ /organelle="plastid"\n+ /mol_type="genomic DNA"\n+ /specimen_voucher="N._Zamora6857-Costa_Rica"\n+ /db_xref="taxon:191923"\n+ /tissue_type="silica"\n+ gene complement(join(101153..101946,72424..72537))\n+ /gene="rps12"\n+ /locus_tag="HHI30_pgp041"\n+ /trans_splicing=""\n+ /db_xref="GeneID:54372102"\n+ CDS complement(join(101153..101178,101715..101946,\n+ 72424..72537))\n+ /gene="rps12"\n+ /locus_tag="HHI30_pgp041"\n+ /trans_splicing=""\n+ /codon_start=1\n+ /transl_table=11\n+ /product="ribosomal protein S12"\n+ /protein_id="YP_009756008.1"\n+ /db_xref="GeneID:54372102"\n+ /translation="MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKP\n+ NSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDA\n+ VGVKDRQQGRSKYGVKKPK"\n+ gene complement(1..74)\n+ /gene="trnH-GUG"\n+ /locus_tag="HHI30_pgt001"\n+ /db_xref="GeneID:54371973"\n+ tRNA complement(1..74)\n+ /gene="trnH-GUG"\n+ /locus_tag="HHI30_pgt001"\n+ /product="tRNA-His"\n+ /db_xref="GeneID:54371973"\n+ repeat_region 1\n+ /gene="rps19"\n+ /locus_t'..b'54501 aataaatcca gtctttcact aagatttcga atagctgtcc cgaattcaag ttgattatgt\n+ 154561 ttcgcctctt cctcggagaa agacgatcaa acaattccca atcatggtcc ttgcggatcg\n+ 154621 gatcatccat ataatataca aaaagaaact ccagatattt gatatctttc tctttgaatg\n+ 154681 agatctcaat tccagcgacg gtttcattag atatcttaca actagaatcc ctcttttttc\n+ 154741 cgatccagtt cctccaccac cgcgaacccc agttagattc aggcatgata cactttttag\n+ 154801 ttattgggag aacccaagta ctctctttcg gatccaggaa agagctctca gagatctttt\n+ 154861 ttccttttgg aagatacagg agcgaaacaa tcaacctatt gatattggaa gactcaaaag\n+ 154921 attcttccaa tgtatcattt ctgggtccaa tggaattcat aggtatagga agaagccctg\n+ 154981 tcaaatagag attttttctt tcgaccatct ttcgattgtt aatacgatat ataaggaccg\n+ 155041 ctactacaaa gagtactaca cccttgatcg tgaaatatcg attgcttgtt gaaccctgtg\n+ 155101 aattgcgtga aagtaggata ctccaaattc gggagtccaa gagttttata aaacgctctt\n+ 155161 gatggaaaaa aatgtgaatg aaagatccca ctgaattgaa ttgggtccat gaatctaaga\n+ 155221 aatagtgaga attcttgatc tctctcaata tctctctcaa ttcgaaaatc caggatttga\n+ 155281 attgatgtcc tttcattgag tcctcctaaa ttgcattgat ttatcctaaa gatttcattt\n+ 155341 caattggaat ttggttattc accatgtacg aggatccccg ctaagcatcc atggctgaat\n+ 155401 ggttaaagcg cccaactcat aattggcgaa ttcgtaggtt caattcctac tggatgcacg\n+ 155461 ccaatgggac cctccaataa gtctattgga attggctctg tatcaatgga atctcatcat\n+ 155521 ccatacataa cgaattggtg tggtatattc atatcataac atatgaacag taagaactag\n+ 155581 cattcttatt gagactagaa ctcataggga agaaaataga tttatggatg gaatcaaata\n+ 155641 tgcagtattt acagacaaaa gtattcggtt attggtgaaa aatcaatata cttctaatgt\n+ 155701 cgaatcagga tcaactagga cagaaataaa gcattgggtc gaactcttct ttggtgtcaa\n+ 155761 ggtaatagct atgaatagtc atcgactccc ggtaaagggt agaagaatgg gacctattat\n+ 155821 gggacataca atgcattaca gacgtatgat cattacgctt caaccgggtt attctattcc\n+ 155881 acctcttaga aagaaaagaa cttaaatcaa aatacttaat agcatggcga tacatttata\n+ 155941 caaaacttct accccgagca cacgcaatgg agccgtagac agtcaagtga aatccaatcc\n+ 156001 acgaaataat ttgatctatg gacagcatcg ttgtggtaaa ggtcgtaatg ccagaggaat\n+ 156061 cattaccgca gggcatagag ggggaggtca taagcgtcta taccgtaaaa tcgattttcg\n+ 156121 acggaatgaa aaagacatat atggtagaat cgtaaccata gaatacgacc ctaatcgaaa\n+ 156181 tgcatacatt tgtctcatac actatgggga tggtgagaaa agatatattt tacatcccag\n+ 156241 aggggctata attggagata ccattgtttc tggtacagaa gttcctataa aaatgggaaa\n+ 156301 tgccctacct ttgagtgcgg tttgaactat tgatttacgt aattggaagt aaccaattag\n+ 156361 gtttacggcg aaacctagaa atcgatcact gatccaattt gagtacctct acaggataga\n+ 156421 cctcaacaga aaactgaaga gtaacggcag caagtgattg agttcagtag ttcctcatat\n+ 156481 aaaattattg actctagaga tatagtaata tggagaagac aaaattgttt caagcaccga\n+ 156541 cagaaccaga agcgcccctt gtttcaaaga ggggaggacg ggttattcac atttcatttg\n+ 156601 atggtcagag gcgaattgaa agctaagcag tggtaattct aaggatttcc cgggggaaaa\n+ 156661 atagagatgt ctcctacgtt acccgtaata tgtggaagta tcgacgtaat ttcatagagt\n+ 156721 cattcggtct gaatgctaca tgaagaacat aagccagatg aaggaacggg aagacctagg\n+ 156781 atgtagaaga tcataacatg agggattcgg cagatttgga ttcctatata tccactcatg\n+ 156841 cggtacttca ttgtacgata tatataagaa ttctacgata tatataagat ccatctgtat\n+ 156901 agatatcatc atctacatcc agaaagccgt atgctttgga agaagcttgt acagtttggg\n+ 156961 aaggggtttt gattgatcaa aaagaagaat ctacttcaac cgatatgccc ttaggcacgg\n+ 157021 ccatacataa catagaaatc acactcggaa agggtggaca attagctaga gcagcaggtg\n+ 157081 ctgtagcgaa actgattgca aaagagggga aatcggccac attaaaatta ccttctgggg\n+ 157141 aggtccgttt gatatccaaa aactgctcag caacagtcgg acaagtgggg aatgttgggg\n+ 157201 taaaccagaa aagtttgggt agagccggat ctaaatgttg gctaggtaag cgtcctgtag\n+ 157261 taagaggagt agttatgaac cctgtagacc atccccatgg gggtggtgaa gggagggccc\n+ 157321 caattggtag aaaaaaaccc gcaactcctt ggggttatcc tgcacttgga agaagaagta\n+ 157381 gaaaaaggaa taaatatagt gataatttga ttcttcgtcg ccgtagtaaa tagtagagta\n+ 157441 gagaaaatag aatttgtttc ttcgtcttta caaaaaaata gggggagtaa gtaaaaaaaa\n+ 157501 taggagtaat gaactgtgac acgttcacta aaaaaaaatc cttttgtagc gaatcattta\n+ 157561 ttaaaaaaaa taaagaagct taacacaaaa gcagaaaaag aaataatagt aacttg\n+//\n' |
| b |
| diff -r 8b330a577046 -r 06bcf65179fb test-data/NC_047400.gb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_047400.gb Thu Feb 23 17:06:37 2023 +0000 |
| b |
| b'@@ -0,0 +1,4672 @@\n+LOCUS NC_047400 158739 bp DNA circular PLN 26-APR-2020\n+DEFINITION Chamaecrista mimosoides voucher Yi15441-KUN plastid, complete\n+ genome.\n+ACCESSION NC_047400\n+VERSION NC_047400.1\n+DBLINK BioProject: PRJNA628455\n+KEYWORDS RefSeq.\n+SOURCE plastid Chamaecrista mimosoides\n+ ORGANISM Chamaecrista mimosoides\n+ Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n+ Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;\n+ Pentapetalae; rosids; fabids; Fabales; Fabaceae; Caesalpinioideae;\n+ Cassia clade; Chamaecrista.\n+REFERENCE 1 (bases 1 to 158739)\n+ AUTHORS Zhang,R., Wang,Y.H., Jin,J.J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.D., Chen,S.Y., Wang,J., Li,D.Z.\n+ and Yi,T.S.\n+ TITLE Exploration of Plastid Phylogenomic Conflict Yields New Insights\n+ into the Deep Relationships of Leguminosae\n+ JOURNAL Syst. Biol. (2020) In press\n+ PUBMED 32065640\n+ REMARK Publication Status: Available-Online prior to print\n+REFERENCE 2 (bases 1 to 158739)\n+ CONSRTM NCBI Genome Project\n+ TITLE Direct Submission\n+ JOURNAL Submitted (26-APR-2020) National Center for Biotechnology\n+ Information, NIH, Bethesda, MD 20894, USA\n+REFERENCE 3 (bases 1 to 158739)\n+ AUTHORS Zhang,R., Wang,Y.-H., Jin,J.-J., Stull,G.W., Bruneau,A., Cardoso,D.,\n+ de Queiroz,L.P., Moore,M.J., Zhang,S.-D., Chen,S.-Y., Wang,J.,\n+ Li,D.-Z. and Yi,T.-S.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (18-NOV-2019) Germplasm Bank of Wild Species, Kunming\n+ Institute of Botany, 132 Lanhei Rd, Kunming, Yunnan 650201, China\n+COMMENT ##Assembly-Data-START##\n+ Assembly Method :: GetOrganelle v. August 25, 2016; CLC\n+ Sequencing Technology :: Illumina\n+ ##Assembly-Data-END##\n+ PROVISIONAL REFSEQ: This record has not yet been subject to final\n+ NCBI review. The reference sequence is identical to MN709886.\n+ Genomics Workbench v. v8.5.1\n+ COMPLETENESS: full length.\n+FEATURES Location/Qualifiers\n+ source 1..158739\n+ /organism="Chamaecrista mimosoides"\n+ /organelle="plastid"\n+ /mol_type="genomic DNA"\n+ /specimen_voucher="Yi15441-KUN"\n+ /db_xref="taxon:948715"\n+ /tissue_type="Fresh"\n+ gene complement(join(102408..103201,74197..74310))\n+ /gene="rps12"\n+ /locus_tag="HJF93_pgp041"\n+ /trans_splicing=""\n+ /db_xref="GeneID:54625455"\n+ CDS complement(join(102408..102433,102970..103201,\n+ 74197..74310))\n+ /gene="rps12"\n+ /locus_tag="HJF93_pgp041"\n+ /trans_splicing=""\n+ /codon_start=1\n+ /transl_table=11\n+ /product="ribosomal protein S12"\n+ /protein_id="YP_009772065.1"\n+ /db_xref="GeneID:54625455"\n+ /translation="MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKP\n+ NSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDA\n+ VGVKDRQQGRSKYGVKKPK"\n+ gene complement(13..86)\n+ /gene="trnH-GUG"\n+ /locus_tag="HJF93_pgt001"\n+ /db_xref="GeneID:54625326"\n+ tRNA complement(13..86)\n+ /gene="trnH-GUG"\n+ /locus_tag="HJF93_pgt001"\n+ /product="tRNA-His"\n+ /db_xref="GeneID:54625326"\n+ gene complement(368..1429)\n+ /gene="psbA"\n+ /locus_tag="HJ'..b'ag ctgtcccgaa\n+ 155641 ttcaagttga ttatgtttcg cctcttcctc ggagaaagac gatcaaacaa ttcccaatca\n+ 155701 tggtccttgc ggatcggatc atccatataa tatacaaaaa gaaactccag atatttgata\n+ 155761 tctttctctt tgaatgagat ctcaattcca gcgacggttt cattagatat cttacaacta\n+ 155821 gaatccctct tttttccgat ccagttcctc caccaccgcg aaccccagtt agattcaggc\n+ 155881 atgatacact ttttagttat tgggagaacc caagtactct ctttcggatc caggaaagag\n+ 155941 ctctcagaga tcttttttcc ttttggaata tacaggagcg aaacaatcaa cctattgata\n+ 156001 ttggaagact caaaagattc ttccaatgta tcatttctgg gtccaatgga attcataggt\n+ 156061 ataggaagaa gccctgtcaa atagagattt tttctttcga ccatctttcg attgttaata\n+ 156121 cgatatataa ggaccgctac taccaagagt actacaccct tgatcgtgaa atatcgattg\n+ 156181 cttgttgaac cctgtgaatt gcgtgaaagt aggatactcc aaattcggga gtccaagagt\n+ 156241 tttataaaac gctcttgatg gaaaaaaatg tgaatgaaag atcccactga attgaattgg\n+ 156301 gtccatgaat ctaagaaata gtgagaattc ttgatctctc tcaatatctc cctcaattcg\n+ 156361 aaaatccagg atttgaattg atgtcctttc attgagtcct cctaaattgc attgatttat\n+ 156421 cctaaagatt tcatttcaat tggaatttgg ttattcacca tgtacaagga tccccgctaa\n+ 156481 gcatccatgg ctgaatggtt aaagcaccca actcataatt ggcgaattcg taggttcaat\n+ 156541 tcctactgga tgcacgccaa tgggaccctc caatacaatt ccaataagtc tattggaatt\n+ 156601 ggctctgtat caatggaatc tcatcatcca tacccaacga attggtgtgg tatattaata\n+ 156661 tcataacata tgaacaataa gaactagcat tcttattgaa actagaactc atagggaaga\n+ 156721 aaattgatat ggatgaaata aaatatgcag tagttacaga caaaagtatt cggttattgg\n+ 156781 tgaaaaatca atatacttct aatgtcgaat caggatcaac taggacagaa ataaagcatt\n+ 156841 gggtcgaact cttctttggt gtcaaggtaa tagctatgaa tagtcatcga ctcccggtaa\n+ 156901 agggtagaag aatgggacct attatgggac atacaatgca ttacagacgt atgatcatta\n+ 156961 cgcttcaacc gggttattct attccacctc ttagaaagaa aagaacttaa atcaaaatac\n+ 157021 ttaatagcat ggcgatacat ttatacaaaa cttctacccc gagcacacgc aatggagccg\n+ 157081 tagacagtca agtgaaatcc aatccacgaa ataatttgat ctatggacaa catcgttgtg\n+ 157141 gtaaaggtcg taatgccaga ggaatcatta ccgcagggca tagaggggga ggtcataagc\n+ 157201 gtctataccg taaaatcgat tttcgacgga atgaaaaaga catatatggt agaatcgtaa\n+ 157261 ccatagaata cgaccctaat cgaaatgcat acatttgtct catacactat ggggatggtg\n+ 157321 agaaaagata tattttacat cccagagggg ctataattgg agataccatt gtttctggta\n+ 157381 cagaagttcc tataaaaatg ggaaatgccc tacctttgag tgcggtttga actattgatt\n+ 157441 tacgtaattg gaagtaacca attaggttta cggcgaaacc tagaaatcga tcactgatcc\n+ 157501 aatttgagta cctctacagg atagacctca tacaggatag acctcaacag aaaactgaag\n+ 157561 agtaacggca gcaagtgatt gagttcagta gttcctcata tcaaattatt gactctagag\n+ 157621 atatagtaat atggagaaga caaaattgtt tcaagcaccg acagaaccag aagcgcccct\n+ 157681 tgtttcaaag aggggaggac gggttattca catttcattt gatggtcaga ggcgaattga\n+ 157741 aagctaagca gtggtaattc taaggattcc ccggggaaaa atagagatgt ctcctacgtt\n+ 157801 acccgtaata tgtggaagtg tcgacgtaat ttcatagagt cattcggtct gaatgctaca\n+ 157861 tgaagaacat aagccagatg aaggaacggg aagacctagg atgtagaaga tcataacatg\n+ 157921 agtgattcgg cagatttgga ttcctatata tccactcatg cggtacttca ttgtacgata\n+ 157981 tataagaatt ctacgatata tataagatcc atctgtatag atatcatcat ctacatccag\n+ 158041 aaagccgtat gctttggaag aagcttgtac agtttgggaa ggggttttga ttgatcaaaa\n+ 158101 agaagaatct acttcaaccg atatgccctt aggcacggcc atacataaca tagaaatcac\n+ 158161 actcggaaag ggtggacaat tagctagagc agcaggtgct gtagcgaaac tgattgcaaa\n+ 158221 agaggggaaa tcggccacat taaaattacc ttctggggag gtccgtttga tatccaaaaa\n+ 158281 ctgctcagca acagtcggac aagtggggaa tgttggggta aaccagaaaa gtttgggtag\n+ 158341 agccggatct aaatgttggc taggtaagcg tcctgtagta agaggagtag ttatgaaccc\n+ 158401 tgtagaccat ccccatgggg gtggtgaagg gagggcccca attggtagaa aaaaacccgc\n+ 158461 aactccttgg ggttatcctg cacttggaag aagaagtaga aaaaggaata aatatagtga\n+ 158521 taatttgatt cttcgtcgcc gtagtaaata gtagagtaga gaaaatcgaa tttgtttctt\n+ 158581 cgtctttaca aaaaaaaaat agggggagta agtaaaaaaa ataggagtaa tgaactgtga\n+ 158641 cacgttcact aaaaaaaaat ccttttgtag cgaatcattt attaagaaaa ataaataagc\n+ 158701 ttaacacaaa agcagaaaaa gaaataatag taacttggt\n+//\n' |