| Previous changeset 3:5784e268efca (2020-08-09) Next changeset 5:bc88856eddab (2022-07-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit f5f8e44e726c9f2cc57e0f0fe8182a73afa56669 |
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modified:
antismash.xml test-data/ARBH01000003.1.cluster001 test-data/index.2.html test-data/index.html |
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added:
macros.xml test-data/annotation.gff3 test-data/index.3.html test-data/sequence_long.fasta test-data/test_02.genbank test-data/test_03.genbank |
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| diff -r 5784e268efca -r e78e25d3b4bd antismash.xml --- a/antismash.xml Sun Aug 09 10:15:12 2020 -0400 +++ b/antismash.xml Tue May 31 14:04:07 2022 +0000 |
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| b'@@ -1,9 +1,10 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool id="antismash" name="Antismash" version="5.1.2" profile="17.01">\n+<tool id="antismash" name="Antismash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>\n- <requirements>\n- <requirement type="package" version="5.1.2">antismash</requirement>\n- </requirements>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'requirements\'/>\n+ <expand macro="bio_tools"/>\n <version_command>antismash --version</version_command>\n <command detect_errors="aggressive">\n <![CDATA[\n@@ -18,6 +19,10 @@\n #end if\n \n ln -s \'$infile\' input_tempfile.$file_extension &&\n+ #if $genefinding_gff3\n+ ln -s $genefinding_gff3 annotation.gff3 &&\n+ #end if\n+\n \n ## create html folder\n mkdir -p \'$htmloutputfolder\' &&\n@@ -25,7 +30,9 @@\n antismash\n --cpus "\\${GALAXY_SLOTS:-12}"\n --taxon \'${cond_taxon.taxon}\'\n-\n+ #if $genefinding_gff3\n+ --genefinding-gff3 annotation.gff3\n+ #end if\n --genefinding-tool $cond_taxon.genefinding_tool\n \n ${cb_general}\n@@ -35,79 +42,112 @@\n --tta-threshold ${tta_threshold}\n ${asf}\n \n- ${extra_cluster}\n ${clusterhmmer}\n ${fullhmmer}\n #if $cond_taxon.taxon == \'fungi\':\n $cond_taxon.cassis\n+ #else \n+ $cond_taxon.tigrfam\n #end if\n \n+ ${cc_mibig}\n+ ${rre}\n+ --logfile $log\n+\n+ ## Advanced options\n+ --minlength $advanced_options.minlength\n+ --hmmdetection-strictness $advanced_options.hmmdetection_strictness\n+ --cb-nclusters $advanced_options.cb_nclusters\n+ --cb-min-homology-scale $advanced_options.cb_min_homology_scale\n+ --rre-cutoff $advanced_options.rre_cutoff\n+ --rre-minlength $advanced_options.rre_minlength\n+\n input_tempfile.$file_extension &&\n \n ## copy all content to html folder\n cp input_tempfile/index.html \'${html}\' 2> /dev/null &&\n cp -r input_tempfile/* \'${htmloutputfolder}\'\n-\n ]]>\n </command>\n <inputs>\n <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>\n+ <param argument="--genefinding-gff3" type="data" format="gff3" optional="true" label="GFF3 file" help="Specify GFF3 file to extract features from" />\n \n <conditional name="cond_taxon">\n- <param argument="--taxon" type="select" label="Origin of DNA">\n+ <param argument="--taxon" type="select" label="Taxonomic classification of input sequence" help="Source of DNA">\n <option value="bacteria" selected="True">Bacteria</option>\n <option value="fungi">Fungi</option>\n </param>\n <when value="bacteria">\n- <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"\n- help="The \'error\' option will raise an error if genefinding is attempted. The \'none\' option will not run genefinding">\n+ <expand macro="genefinding">\n <option value="prodigal" selected="True">Prodigal</option>\n <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>\n- <option value="glimmerhmm">GlimmerHMM</option>\n- <option value="none">None</option>\n- <option value="error">Error</option>\n- </param>\n+ </expand>\n+ <param argument="--tigrfam" type="boolean" truevalue="--tigrfam" falsevalue="" checked="false" \n+ label="Annota'..b'{tool.name} on ${on_string} (all files compressed)">\n+ <collection name="archive" type="list" label="${tool.name} on ${on_string}: all files compressed">\n <discover_datasets pattern="(?P<designation>.*)\\.zip" directory="input_tempfile" ext="zip" visible="false" />\n <filter>\'all\' in outputs</filter>\n </collection>\n- <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />\n+ <data format="html" name="html" label="${tool.name} on ${on_string}: HTML report" />\n+ <data format="txt" name="log" label="${tool.name} on ${on_string}: log file">\n+ <filter>\'log\' in outputs</filter>\n+ </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="infile" value="sequence.fasta"/>\n <output name="html" file="index.html"/>\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="infile" value="sequence.gb"/>\n <param name="outputs" value="html,gb"/>\n <param name="taxon" value="fungi"/>\n- <param name="clusterhmmer" value="True"/>\n- <param name="fullhmmer" value="True"/>\n- <param name="extra_cluster" value="--cf-create-clusters"/>\n- <param name="cassis" value="True"/>\n- <param name="cb_general" value="True"/>\n+ <param name="clusterhmmer" value="true"/>\n+ <param name="fullhmmer" value="true"/>\n+ <param name="cassis" value="true"/>\n+ <param name="cb_general" value="true"/>\n <output_collection name="genbank" type="list">\n- <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" />\n- <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/>\n+ <element name="input_tempfile" file="test_02.genbank" ftype="genbank" lines_diff="2"/>\n </output_collection>\n- <output name="html" file="index.2.html"/>\n+ <output name="html" file="index.2.html" ftype="html">\n+ <assert_contents>\n+ <has_text text="No results found on input"/>\n+ </assert_contents>\n+ </output>\n </test>\n+\n+ <test expect_num_outputs="3">\n+ <param name="infile" value="sequence_long.fasta"/>\n+ <param name="genefinding_gff3" value="annotation.gff3"/>\n+ <param name="fullhmmer" value="true"/>\n+ <param name="cc_mibig" value="true"/>\n+ <param name="pfam2go" value="true"/>\n+ <param name="rre" value="true"/>\n+ <param name="outputs" value="html,gb,log"/>\n+ <section name="advanced_options">\n+ <param name="minlength" value="1000"/>\n+ <param name="hmmdetection_strictness" value="strict"/>\n+ <param name="cb_nclusters" value="10"/>\n+ <param name="cb_min_homology_scale" value="0.1"/>\n+ <param name="rre_cutoff" value="10"/>\n+ <param name="rre_minlength" value="50"/>\n+ </section>\n+ <output_collection name="genbank" type="list">\n+ <element name="input_tempfile" file="test_03.genbank" ftype="genbank" lines_diff="2"/>\n+ </output_collection>\n+ <output name="html" file="index.3.html" ftype="html">\n+ <assert_contents>\n+ <has_text text="No results found on input"/>\n+ </assert_contents>\n+ </output>\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="antiSMASH status: SUCCESS"/>\n+ <has_text text="HMM detection using strictness: strict"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ \n </tests>\n <help>\n <![CDATA[\n@@ -195,7 +274,5 @@\n \n ]]>\n </help>\n- <citations>\n- <citation type="doi">10.1093/nar/gkv437</citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 5784e268efca -r e78e25d3b4bd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 31 14:04:07 2022 +0000 |
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| @@ -0,0 +1,28 @@ +<macros> + <token name="@TOOL_VERSION@">6.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">antismash</requirement> + </requirements> + </xml> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">antismash</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">>10.1093/nar/gkv437</citation> + </citations> + </xml> + <xml name="genefinding"> + <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding" + help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding"> + <yield/> + <option value="glimmerhmm">GlimmerHMM</option> + <option value="none">None</option> + <option value="error">Error</option> + </param> + </xml> +</macros> |
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| diff -r 5784e268efca -r e78e25d3b4bd test-data/ARBH01000003.1.cluster001 --- a/test-data/ARBH01000003.1.cluster001 Sun Aug 09 10:15:12 2020 -0400 +++ b/test-data/ARBH01000003.1.cluster001 Tue May 31 14:04:07 2022 +0000 |
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| b'@@ -3,11 +3,80 @@\n A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.\n ACCESSION ARBH01000003\n VERSION ARBH01000003.1\n-KEYWORDS .\n+DBLINK BioProject: PRJNA165347\n+ BioSample: SAMN02256403\n+KEYWORDS WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.\n SOURCE Amycolatopsis balhimycina FH 1894\n ORGANISM Amycolatopsis balhimycina FH 1894\n Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;\n Amycolatopsis.\n+REFERENCE 1 (bases 1 to 3500)\n+ AUTHORS Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N.,\n+ Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N.,\n+ Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N.,\n+ Hua,S.X. and Woyke,T.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell\n+ Drive, Walnut Creek, CA 94598-1698, USA\n+COMMENT ##MIGS-Data-START##\n+ investigation_type :: bacteria_archaea\n+ project_name :: Amycolatopsis balhimycina DSM 44591\n+ collection_date :: Missing\n+ lat_lon :: Missing\n+ depth :: Missing\n+ alt_elev :: Missing\n+ country :: India\n+ num_replicons :: Missing\n+ ref_biomaterial :: DSM 44591\n+ biotic_relationship :: Free living\n+ rel_to_oxygen :: Aerobe\n+ isol_growth_condt :: Missing\n+ assembly :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. 4.24\n+ finishing_strategy :: Missing\n+ environment :: Soil\n+ trophic_level :: Missing\n+ sequencing_meth :: WGS\n+ GOLD Stamp ID :: Gi10728\n+ Type Strain :: Yes\n+ Funding Program :: DOE-CSP 2011\n+ Isolation Site :: Soil\n+ Cell Shape :: Filament-shaped\n+ Motility :: Nonmotile\n+ Sporulation :: Sporulating\n+ Temperature Range :: Mesophile\n+ Gram Staining :: Gram+\n+ Diseases :: None\n+ ##MIGS-Data-END##\n+ ##Genome-Assembly-Data-START##\n+ Finishing Goal :: Improved High-Quality Draft\n+ Current Finishing Status :: Improved High-Quality Draft\n+ Assembly Method :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v.\n+ 4.24\n+ Genome Coverage :: Unknown\n+ Sequencing Technology :: Illumina GAii\n+ ##Genome-Assembly-Data-END##\n+ URL -- http://www.jgi.doe.gov\n+ JGI Project ID: 404843\n+ Source DNA and Organism available from Hans-Peter Klenk\n+ (hpk@dsmz.de)\n+ Source DNA available from Hans-Peter Klenk (hpk@dsmz.de)\n+ Organism available from Hans-Peter Klenk (hpk@dsmz.de)\n+ Contacts: Hans-Peter Klenk (hpk@dsmz.de)\n+ Tanja Woyke (microbe@cuba.jgi-psf.org)\n+ Whole genome sequencing and draft assembly at JGI-PGF\n+ Annotation by JGI-ORNL\n+ The JGI and collaborators endorse the principles for the\n+ distribution and use of large scale sequencing data adopted by the\n+ larger genome sequencing community and urge users of this data to\n+ follow them. It is our intention to publish the work of this\n+ project in a timely fashion and we welcome collaborative\n+ interaction on the project and analysis.\n+ (http://www.genome.gov/page.cfm?pageID=10506376)\n+ Full annotations are available from IMG.\n+ ##antiSMASH-Data-START##\n+ Version :: 6.1.0\n+ Run date :: 2022-'..b'otifs"\n- /detection="hmmscan"\n- /evalue="3.20E-03"\n- /label="PKSI-AT-mM_m2"\n- /locus_tag="ctg1_1"\n- /motif="PKSI-AT-mM_m2"\n- /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,\n- bit-score: 10.9)"\n- /score="10.9"\n- /translation="DETGYTQPALFAFEVALFRLL"\n- CDS_motif 3105..3227\n- /aSTool="pksnrpsmotif"\n- /asDomain_id="nrpspksmotif_ctg1_1_0008"\n- /database="abmotifs"\n- /detection="hmmscan"\n- /evalue="2.30E-22"\n- /label="PKSI-AT-M_m3"\n- /locus_tag="ctg1_1"\n- /motif="PKSI-AT-M_m3"\n- /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,\n- bit-score: 71.3)"\n- /score="71.3"\n- /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"\n- CDS_motif 3312..3350\n- /aSTool="pksnrpsmotif"\n- /asDomain_id="nrpspksmotif_ctg1_1_0009"\n- /database="abmotifs"\n- /detection="hmmscan"\n- /evalue="4.70E-04"\n- /label="PKSI-AT-M_m5"\n- /locus_tag="ctg1_1"\n- /motif="PKSI-AT-M_m5"\n- /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,\n- bit-score: 13.4)"\n- /score="13.4"\n- /translation="AAVNGPESVVLAG"\n+ CDS complement(170..3134)\n+ /ID="input.cds1.1"\n+ /Name="input.path1.gene1"\n+ /Note="initial-exon"\n+ /gene="input.path1.gene1"\n+ /phase="0"\n+ /source="GlimmerHMM"\n+ /transl_table=1\n+ /translation="MPGQVIRRHTPRLQQPEQRHLEGEQRRLGVPRLVEGRGIVVPHHV\n+ PQRTGQVEVPQHRVQRVGEHRVALVQLAAHPGPLAALAGEQERRAAPRHGAPHHAAVRL\n+ VAGQCGQAAPQFVVVLGQQHRTVFEGRPGGGQRVPEHGRRHAVVQGVQHGGGLSAQRCF\n+ RPAGQRDRHQAGLRLGAGFGGRFRGLLEDGVHVRAAQPEGRDTGPARPAALRPRHAAGR\n+ QLDRAGAPVDVRGGLVHVQRLGYQPVPQRLHHLDHAGHAGGHLGVADVGLHRAEQQRPF\n+ PVLAVGGQQGLGLDRVAQRGAGAVALDHVHLGRREPRVGQRLPDHPLLGRAAGRGHAVG\n+ RAVLVRGRTPDHRQDPVPVALRVGQLLQQHQADALAEGHAVGPVRVGLATAVRGQCALA\n+ READERPRRRHHAHPAGQRQAALPRPQRLRGQVDGDQRRRAGGVQGDRRALQPEQVGEP\n+ AGQDAAQRAGDHVAVGVVHRAGHGRGVVLVAGPDEGAGAAAPQRVRVDPGPLERLPRRL\n+ QQQALLRIHGQCLPRRDAEEARVELGRLVQEAALHRIGLAAGVRVRVVERVGRPVAVGR\n+ EAGDGVHAAHDQVPQPFRGVRATRVAAGHPDDGDGLAGVHAGHGRCLLDGTRAGDRGGQ\n+ EPGQPPRRRVVEHHGGGQGQAGAGGDPVAQVDRGDRVEADVAEGAVLGQRVGRRVAQHG\n+ RGLGPDQFQEQVGALGLGQRAQPGGELAAGAGGGRGGGGLGEPPHLRQLVEQQRRPDGG\n+ VDRVVPLPVQIGHGQRGLVVVQGPAQTLQRQLRRHEHQAAAHDLLRVDPAEFAVVGPDA\n+ PRQRGGPQPPGAPVGCQRVQVRVAGHVGGVRAGAPQAGGGGVQHERIELVGVEQLVQVA\n+ RAHHLGVHGPGERGQVGLGQRVQLDHGGRVHHVPHGPALGPQPRQQGGQRRLVGDVAGH\n+ RLDGLAQLRQQLPGLRGLGAGAAGQHDVLGALLGQPAGQVRGQGAGAAGDQRGAARGP"\n+ CDS 3249..3404\n+ /ID="input.cds2.1"\n+ /Name="input.path1.gene2"\n+ /Note="initial-exon"\n+ /gene="input.path1.gene2"\n+ /phase="0"\n+ /source="GlimmerHMM"\n+ /transl_table=1\n+ /translation="MVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAVLQAAGR\n+ LEAAGHK"\n ORIGIN\n 1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg\n 61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg\n' |
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| diff -r 5784e268efca -r e78e25d3b4bd test-data/annotation.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation.gff3 Tue May 31 14:04:07 2022 +0000 |
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| b'@@ -0,0 +1,1000 @@\n+##gff-version 3\n+##sequence-region Chromosome 1 4641652\n+#!genome-build ASM584v2\n+#!genome-version ASM584v2\n+#!genome-build-accession GCA_000005845.2\n+#!genebuild-last-updated 2018-09\n+Chromosome\tASM584v2\tchromosome\t1\t4641652\t.\t.\t.\tID=chromosome:Chromosome;Alias=U00096.3;Is_circular=true\n+###\n+Chromosome\tena\tgene\t190\t255\t.\t+\t.\tID=gene:b0001;Name=thrL;biotype=protein_coding;description=thr operon leader peptide;gene_id=b0001;logic_name=ena\n+Chromosome\tena\tmRNA\t190\t255\t.\t+\t.\tID=transcript:AAC73112;Parent=gene:b0001;Name=thrL-1;biotype=protein_coding;transcript_id=AAC73112\n+Chromosome\tena\texon\t190\t255\t.\t+\t.\tParent=transcript:AAC73112;Name=AAC73112-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73112-1;rank=1\n+Chromosome\tena\tCDS\t190\t255\t.\t+\t0\tID=CDS:AAC73112;Parent=transcript:AAC73112;protein_id=AAC73112\n+###\n+Chromosome\tena\tgene\t337\t2799\t.\t+\t.\tID=gene:b0002;Name=thrA;biotype=protein_coding;description=fused aspartate kinase/homoserine dehydrogenase 1;gene_id=b0002;logic_name=ena\n+Chromosome\tena\tmRNA\t337\t2799\t.\t+\t.\tID=transcript:AAC73113;Parent=gene:b0002;Name=thrA-1;biotype=protein_coding;transcript_id=AAC73113\n+Chromosome\tena\texon\t337\t2799\t.\t+\t.\tParent=transcript:AAC73113;Name=AAC73113-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73113-1;rank=1\n+Chromosome\tena\tCDS\t337\t2799\t.\t+\t0\tID=CDS:AAC73113;Parent=transcript:AAC73113;protein_id=AAC73113\n+###\n+Chromosome\tena\tgene\t2801\t3733\t.\t+\t.\tID=gene:b0003;Name=thrB;biotype=protein_coding;description=homoserine kinase;gene_id=b0003;logic_name=ena\n+Chromosome\tena\tmRNA\t2801\t3733\t.\t+\t.\tID=transcript:AAC73114;Parent=gene:b0003;Name=thrB-1;biotype=protein_coding;transcript_id=AAC73114\n+Chromosome\tena\texon\t2801\t3733\t.\t+\t.\tParent=transcript:AAC73114;Name=AAC73114-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73114-1;rank=1\n+Chromosome\tena\tCDS\t2801\t3733\t.\t+\t0\tID=CDS:AAC73114;Parent=transcript:AAC73114;protein_id=AAC73114\n+###\n+Chromosome\tena\tgene\t3734\t5020\t.\t+\t.\tID=gene:b0004;Name=thrC;biotype=protein_coding;description=threonine synthase;gene_id=b0004;logic_name=ena\n+Chromosome\tena\tmRNA\t3734\t5020\t.\t+\t.\tID=transcript:AAC73115;Parent=gene:b0004;Name=thrC-1;biotype=protein_coding;transcript_id=AAC73115\n+Chromosome\tena\texon\t3734\t5020\t.\t+\t.\tParent=transcript:AAC73115;Name=AAC73115-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73115-1;rank=1\n+Chromosome\tena\tCDS\t3734\t5020\t.\t+\t0\tID=CDS:AAC73115;Parent=transcript:AAC73115;protein_id=AAC73115\n+###\n+Chromosome\tena\tgene\t5234\t5530\t.\t+\t.\tID=gene:b0005;Name=yaaX;biotype=protein_coding;description=DUF2502 domain-containing protein YaaX;gene_id=b0005;logic_name=ena\n+Chromosome\tena\tmRNA\t5234\t5530\t.\t+\t.\tID=transcript:AAC73116;Parent=gene:b0005;Name=yaaX-1;biotype=protein_coding;transcript_id=AAC73116\n+Chromosome\tena\texon\t5234\t5530\t.\t+\t.\tParent=transcript:AAC73116;Name=AAC73116-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73116-1;rank=1\n+Chromosome\tena\tCDS\t5234\t5530\t.\t+\t0\tID=CDS:AAC73116;Parent=transcript:AAC73116;protein_id=AAC73116\n+###\n+Chromosome\tena\tgene\t5683\t6459\t.\t-\t.\tID=gene:b0006;Name=yaaA;biotype=protein_coding;description=peroxide stress resistance protein YaaA;gene_id=b0006;logic_name=ena\n+Chromosome\tena\tmRNA\t5683\t6459\t.\t-\t.\tID=transcript:AAC73117;Parent=gene:b0006;Name=yaaA-1;biotype=protein_coding;transcript_id=AAC73117\n+Chromosome\tena\texon\t5683\t6459\t.\t-\t.\tParent=transcript:AAC73117;Name=AAC73117-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73117-1;rank=1\n+Chromosome\tena\tCDS\t5683\t6459\t.\t-\t0\tID=CDS:AAC73117;Parent=transcript:AAC73117;protein_id=AAC73117\n+###\n+Chromosome\tena\tgene\t6529\t7959\t.\t-\t.\tID=gene:b0007;Name=yaaJ;biotype=protein_coding;description=putative transporter YaaJ;gene_id=b0007;logic_name=ena\n+Chromosome\tena\tmRNA\t6529\t7959\t.\t-\t.\tID=transcript:AAC73118;Parent=gene:b0007;Name=yaaJ-1;biotype=protein_coding;transcript_id=AAC73118\n+Chromosome\tena\texon\t6529\t7959\t.\t-\t.\tParent=transcript:AAC73118;Name=AAC73118-1;con'..b'on_id=AAC73300-1;rank=1\n+Chromosome\tena\tCDS\t213678\t213932\t.\t-\t0\tID=CDS:AAC73300;Parent=transcript:AAC73300;protein_id=AAC73300\n+###\n+Chromosome\tena\tgene\t213925\t214125\t.\t-\t.\tID=gene:b4406;Name=yaeP;biotype=protein_coding;description=UPF0253 family protein YaeP;gene_id=b4406;logic_name=ena\n+Chromosome\tena\tmRNA\t213925\t214125\t.\t-\t.\tID=transcript:AAT48124;Parent=gene:b4406;Name=yaeP-1;biotype=protein_coding;transcript_id=AAT48124\n+Chromosome\tena\texon\t213925\t214125\t.\t-\t.\tParent=transcript:AAT48124;Name=AAT48124-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAT48124-1;rank=1\n+Chromosome\tena\tCDS\t213925\t214125\t.\t-\t0\tID=CDS:AAT48124;Parent=transcript:AAT48124;protein_id=AAT48124\n+###\n+Chromosome\tena\tgene\t214291\t214836\t.\t+\t.\tID=gene:b0190;Name=yaeQ;biotype=protein_coding;description=uncharacterized protein YaeQ;gene_id=b0190;logic_name=ena\n+Chromosome\tena\tmRNA\t214291\t214836\t.\t+\t.\tID=transcript:AAC73301;Parent=gene:b0190;Name=yaeQ-1;biotype=protein_coding;transcript_id=AAC73301\n+Chromosome\tena\texon\t214291\t214836\t.\t+\t.\tParent=transcript:AAC73301;Name=AAC73301-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73301-1;rank=1\n+Chromosome\tena\tCDS\t214291\t214836\t.\t+\t0\tID=CDS:AAC73301;Parent=transcript:AAC73301;protein_id=AAC73301\n+###\n+Chromosome\tena\tgene\t214833\t215255\t.\t+\t.\tID=gene:b0191;Name=arfB;biotype=protein_coding;description=peptidyl-tRNA hydrolase%2C ribosome rescue factor;gene_id=b0191;logic_name=ena\n+Chromosome\tena\tmRNA\t214833\t215255\t.\t+\t.\tID=transcript:AAC73302;Parent=gene:b0191;Name=arfB-1;biotype=protein_coding;transcript_id=AAC73302\n+Chromosome\tena\texon\t214833\t215255\t.\t+\t.\tParent=transcript:AAC73302;Name=AAC73302-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73302-1;rank=1\n+Chromosome\tena\tCDS\t214833\t215255\t.\t+\t0\tID=CDS:AAC73302;Parent=transcript:AAC73302;protein_id=AAC73302\n+###\n+Chromosome\tena\tgene\t215269\t215979\t.\t+\t.\tID=gene:b0192;Name=nlpE;biotype=protein_coding;description=lipoprotein NlpE;gene_id=b0192;logic_name=ena\n+Chromosome\tena\tmRNA\t215269\t215979\t.\t+\t.\tID=transcript:AAC73303;Parent=gene:b0192;Name=nlpE-1;biotype=protein_coding;transcript_id=AAC73303\n+Chromosome\tena\texon\t215269\t215979\t.\t+\t.\tParent=transcript:AAC73303;Name=AAC73303-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73303-1;rank=1\n+Chromosome\tena\tCDS\t215269\t215979\t.\t+\t0\tID=CDS:AAC73303;Parent=transcript:AAC73303;protein_id=AAC73303\n+###\n+Chromosome\tena\tgene\t216179\t217003\t.\t-\t.\tID=gene:b0193;Name=yaeF;biotype=protein_coding;description=peptidase C92 family protein;gene_id=b0193;logic_name=ena\n+Chromosome\tena\tmRNA\t216179\t217003\t.\t-\t.\tID=transcript:AAC73304;Parent=gene:b0193;Name=yaeF-1;biotype=protein_coding;transcript_id=AAC73304\n+Chromosome\tena\texon\t216179\t217003\t.\t-\t.\tParent=transcript:AAC73304;Name=AAC73304-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73304-1;rank=1\n+Chromosome\tena\tCDS\t216179\t217003\t.\t-\t0\tID=CDS:AAC73304;Parent=transcript:AAC73304;protein_id=AAC73304\n+###\n+Chromosome\tena\tgene\t217057\t218775\t.\t-\t.\tID=gene:b0194;Name=proS;biotype=protein_coding;description=proline--tRNA ligase;gene_id=b0194;logic_name=ena\n+Chromosome\tena\tmRNA\t217057\t218775\t.\t-\t.\tID=transcript:AAC73305;Parent=gene:b0194;Name=proS-1;biotype=protein_coding;transcript_id=AAC73305\n+Chromosome\tena\texon\t217057\t218775\t.\t-\t.\tParent=transcript:AAC73305;Name=AAC73305-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73305-1;rank=1\n+Chromosome\tena\tCDS\t217057\t218775\t.\t-\t0\tID=CDS:AAC73305;Parent=transcript:AAC73305;protein_id=AAC73305\n+###\n+Chromosome\tena\tgene\t218887\t219594\t.\t-\t.\tID=gene:b0195;Name=trmO;biotype=protein_coding;description=tRNA m(6)t(6)A37 methyltransferase;gene_id=b0195;logic_name=ena\n+Chromosome\tena\tmRNA\t218887\t219594\t.\t-\t.\tID=transcript:AAC73306;Parent=gene:b0195;Name=trmO-1;biotype=protein_coding;transcript_id=AAC73306\n+Chromosome\tena\texon\t218887\t219594\t.\t-\t.\tParent=transcript:AAC73306;Name=AAC73306-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AAC73306-1;rank=1\n' |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/index.2.html --- a/test-data/index.2.html Sun Aug 09 10:15:12 2020 -0400 +++ b/test-data/index.2.html Tue May 31 14:04:07 2022 +0000 |
| [ |
| @@ -29,7 +29,7 @@ </div> <div> <a href="https://fungismash.secondarymetabolites.org/"> - antiSMASH version 5.1.2 + antiSMASH version 6.1.1 </a> </div> </div> @@ -91,7 +91,7 @@ <script src="regions.js"></script> <script> $(document).ready(function() { - viewer["start"](all_regions, details_data, recordData); + viewer["start"](all_regions, details_data, resultsData, recordData); }) </script> |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/index.3.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.3.html Tue May 31 14:04:07 2022 +0000 |
| [ |
| @@ -0,0 +1,114 @@ + +<!doctype html> +<html lang="en"> +<head> + <meta charset="utf-8" /> + <title>input_tempfile - 0 region(s) - antiSMASH results</title> + <style>img {width: 20px; height: 20px;}</style> + <link rel="stylesheet" type="text/css" href="css/bacteria.css"> + <meta property="og:title" content="input_tempfile - 0 record(s) - 0 region(s)" /> + <meta property="og:description" content=""> + <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/bacteria_logo.png" /> + <meta property="og:image:alt" content="antiSMASH logo" /> + <meta property="og:image:width" content="600" /> + <meta property="og:image:height" content="600" /> + <meta property="og:url" content="https://antismash.secondarymetabolites.org/upload/input_tempfile/index.html" /> + <meta property="og:type" content="website" /> + <meta name="twitter:card" content="summary" /> + <meta name="twitter:site" content="@antismash_dev" /> +</head> + +<body> + <div id="header"> + <nav> + <div class="main-link"> + <div> + <a href="https://antismash.secondarymetabolites.org/"> + <img src="images/bacteria_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;"> + </a> + </div> + <div> + <a href="https://antismash.secondarymetabolites.org/"> + antiSMASH version 6.1.1 + </a> + </div> + </div> + <div class="custom-description"></div> + <div class="ancillary-links"> + <div class="ancillary-link dropdown-menu" id="download-dropdown"><a href="#" id="download-dropdown-link"><img src="images/download.svg" alt="download"> Download</a> + <ul class="dropdown-options"> + + <li><a href="input_tempfile.zip">Download all results</a></li> + + <li><a href="input_tempfile.gbk">Download GenBank summary file</a></li> + + </ul> + </div> + <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.org/#!/about"><img src="images/about.svg" alt="about"> About</a></div> + <div class="ancillary-link"><a href="https://docs.antismash.secondarymetabolites.org/"><img src="images/help.svg" alt="help"> Help</a></div> + <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.org/#!/contact"><img src="images/contact.svg" alt="contact"> Contact</a></div> + </div> + </nav> + <div id="buttons"> + <span id="region-type">Select genomic region:</span> + <div id="regionbuttons"> + <div class="arrow-left" id="prev-region"></div> + <div class="regbutton" style="min-width: inherit;"><a href="#">Overview</a></div> + <div style="display: flex; flex-wrap: wrap"> + + </div> + <div id="last-regbutton"><div class="arrow-right" id="next-region"></div></div> + </div> + </div> + </div> + + <!-- overview page --> + + <div class="page" id="overview"> + <div class="no-results">No results found on input.</div> + </div> + + + + + + <footer class="footer"> + <div class="container"> + <div> + <img src="images/bacteria_antismash_logo.svg" style="height:90px;width:unset;"> + </div> + <div class="cite-me"> + If you have found antiSMASH useful, please <a href="https://antismash.secondarymetabolites.org/#!/about">cite us</a>. + </div> + <div> + <img src="images/bacteria_antismash_icon.svg" style="height:100px;width:unset;"> + </div> + </div> + </footer> + + <script src="js/jquery.js"></script> + <script src="js/antismash.js"></script> + <script src="regions.js"></script> + <script> + $(document).ready(function() { + viewer["start"](all_regions, details_data, resultsData, recordData); + }) + </script> + +<svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink"> + <defs> + <filter id="inset-shadow"> + <feOffset dx="-2" dy="-2"></feOffset> + <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur> + <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite> + <feFlood flood-color="black" result="color" flood-opacity="1"></feFlood> + <feComposite operator="in" in="color" in2="inverse" result="shadow"></feComposite> + <feComponentTransfer in="shadow" result="shadow"> + <feFuncA type="linear" slope=".95"></feFuncA> + </feComponentTransfer> + <feComposite operator="over" in="shadow" in2="SourceGraphic"></feComposite> + </filter> + </defs> +</svg> +</body> +</html> \ No newline at end of file |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/index.html --- a/test-data/index.html Sun Aug 09 10:15:12 2020 -0400 +++ b/test-data/index.html Tue May 31 14:04:07 2022 +0000 |
| [ |
| @@ -29,7 +29,7 @@ </div> <div> <a href="https://antismash.secondarymetabolites.org/"> - antiSMASH version 5.1.2 + antiSMASH version 6.1.1 </a> </div> </div> @@ -57,9 +57,7 @@ <div style="display: flex; flex-wrap: wrap"> - - - <div class="regbutton T1PKS r1c1"> + <div class="regbutton PKS T1PKS r1c1"> <a href="#r1c1">1.1</a> </div> @@ -81,7 +79,11 @@ <div id="record-tables"> <div id="single-record-tables"> <div class="record-overview-header"> - <strong>ARBH01000003.1</strong> + <strong>ARBH01000003.1</strong> + <div class="download-container"> + <div class="download-icon-inverse download-svg" data-tag="record-minimap-1" data-filename="ARBH01000003.1_overview.svg"> + </div> + </div> </div> <div class="record-overview-details"> <svg id="record-minimap-1" class="record-overview-svg" height="1" width="1"></svg> @@ -98,9 +100,7 @@ </thead> <tbody> <tr class="linked-row odd" data-anchor="#r1c1"> - - - <td class="regbutton T1PKS r1c1"> + <td class="regbutton PKS T1PKS r1c1"> <a href="#r1c1">Region 1</a> </td> <td> @@ -139,6 +139,9 @@ <div class="region-download"> <a href = ARBH01000003.1.region001.gbk>Download region GenBank file</a> </div> + <div class="region-download"> + <div class="link-like download-svg" data-tag="r1c1-svg" data-filename="ARBH01000003.1_r1c1.svg">Download region SVG</div> + </div> <div class = 'description-text'> Location: 1 - 3,500 nt. (total: 3,500 nt) @@ -199,7 +202,6 @@ </div> - </div> </div> <div class="zoom-buttons"> @@ -231,8 +233,6 @@ - - <div class="body-details-header r1c1-knownclusterblast" data-name="r1c1-knownclusterblast"> KnownClusterBlast </div> @@ -242,6 +242,8 @@ </div> + + </div> @@ -250,6 +252,10 @@ <div class="heading"> <span>Detailed domain annotation</span> <div class="help-container"> <div class="help-icon" data-id="nrps-domain-help-1"></div> <span class="help-tooltip" id="nrps-domain-help-1">Shows <a href='https://docs.antismash.secondarymetabolites.org/glossary/#nrps' target='_blank'>NRPS</a>- and <a href='https://docs.antismash.secondarymetabolites.org/glossary/#pks' target='_blank'>PKS</a>-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.<br>A glossary is available <a href='https://docs.antismash.secondarymetabolites.org/modules/nrps_pks_domains/' target='_blank'>here</a>.</span></div> + <div class="download-container"> + <div class="download-icon download-svg" data-tag="r1c1-details-svg" data-filename="ARBH01000003.1_r1c1_nrps_pks.svg"> + </div> + </div> </div> <div class="nrps-pks-domain-buttons"> <div class="domains-selected-only switch-container"><span class="switch-desc">Selected features only</span> <label class="switch"> <input class="domains-selected-only" type="checkbox"> <span class="slider"></span> </label></div> @@ -261,8 +267,6 @@ - - <div class="body-details-section r1c1-knownclusterblast"> <div class = "knownclusterblast"> <div class="heading"> @@ -292,6 +296,8 @@ </div> + + </div> <div class="sidepanel"> @@ -337,7 +343,7 @@ <script src="regions.js"></script> <script> $(document).ready(function() { - viewer["start"](all_regions, details_data, recordData); + viewer["start"](all_regions, details_data, resultsData, recordData); }) </script> |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/sequence_long.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence_long.fasta Tue May 31 14:04:07 2022 +0000 |
| b |
| b'@@ -0,0 +1,10000 @@\n+>Chromosome dna:chromosome chromosome:ASM584v2:Chromosome:1:4641652:1 REF\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC\n+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG\n+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC\n+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT\n+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG\n+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT\n+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG\n+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA\n+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG\n+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT\n+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA\n+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC\n+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA\n+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC\n+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC\n+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG\n+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC\n+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT\n+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC\n+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG\n+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG\n+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG\n+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG\n+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC\n+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC\n+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG\n+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA\n+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT\n+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC\n+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC\n+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG\n+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC\n+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA\n+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC\n+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG\n+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT\n+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG\n+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT\n+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG\n+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG\n+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT\n+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC\n+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT\n+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA\n+GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA\n+AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT\n+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT\n+GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT\n+TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG\n+GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT\n+GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA\n+AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA\n+GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT\n+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA\n+CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT\n+ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTG'..b'CAGCGCGCGGTGCATATTCTGCTGGTTTCT\n+AATGTCGCGCAAAGCTATTTCAATCAGCAACTGGCGTATGCGCAATTGCAAATAGCCGAA\n+GAAACGCTGCGTAATTATCAGCAGTCATATGCGTTTGTCGAAAAACAACTGTTGACAGGT\n+AGCAGTAATGTTCTGGCGCTGGAACAGGCTCGCGGGGTGATAGAAAGTACCCGCAGCGAC\n+ATCGCTAAACGTCAGGGGGAACTGGCGCAGGCGAATAATGCATTGCAACTGTTGCTGGGA\n+AGCTACGGCAAGCTGCCGCAAGCGCAGACAGTAAACAGCGACAGCCTGCAAAGCGTTAAA\n+TTACCGGCGGGATTGTCGTCGCAAATCTTATTGCAGCGCCCGGATATTATGGAAGCTGAA\n+CACGCGTTAATGGCGGCTAATGCCAATATTGGCGCTGCACGCGCGGCATTTTTTCCGTCT\n+ATAAGCCTGACCAGCGGAATATCGACCGCCAGTAGCGATCTATCGTCATTATTTAACGCC\n+AGCAGCGGGATGTGGAATTTTATACCCAAAATTGAGATCCCCATTTTTAATGCCGGACGC\n+AACCAGGCCAATCTGGATATCGCCGAAATTCGCCAGCAGCAGTCGGTGGTGAATTATGAA\n+CAGAAAATCCAGAACGCCTTTAAAGAAGTGGCAGATGCGCTGGCATTACGTCAAAGCCTG\n+AACGATCAAATTAGCGCCCAGCAGCGTTATCTGGCATCGCTGCAAATTACTTTGCAACGG\n+GCGCGGGCATTATATCAGCACGGCGCAGTAAGTTATCTGGAAGTGCTGGATGCCGAGCGT\n+TCTTTATTTGCAACCCGACAAACTTTACTTGATCTGAATTATGCCCGTCAGGTTAACGAA\n+ATTTCTTTGTATACCGCACTTGGTGGCGGTTGACAGCAATATACTCGTCATACTTCAAGT\n+TGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGA\n+TTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAG\n+GAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGG\n+CTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGT\n+TATTAGCGCCACTGGCGTGGTAAAGGGTATCGATCTGGAAAGCAAAAAAATCACCATCCA\n+TCACGATCCGATTGCTGCCGTGAACTGGCCGGAGATGACCATGCGCTTTACCATCACCCC\n+GCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCA\n+GGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGAT\n+GAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTCTGCGGCAGG\n+TTTTACCTGGGTTGCAAAGGCGGAACCGCCTGCAGAAAAAACGTCGACCGCAGAACGTAA\n+AATCTTATTCTGGTACGACCCAATGTATCCCAATACGCGGTTCGATAAACCAGGTAAATC\n+GCCGTTTATGGATATGGATCTGGTGCCGAAATATGCCGATGAAGAGAGTTCTGCGTCTGG\n+TGTGCGCATTGACCCGACTCAGACGCAGAATCTGGGGGTGAAAACGGCTACCGTCACGCG\n+CGGACCGCTGACTTTTGCCCAGAGTTTCCCGGCGAATGTCAGTTACAACGAGTATCAGTA\n+TGCCATTGTGCAGGCTCGCGCTGCCGGGTTTATCGACAAGGTGTATCCGCTTACCGTGGG\n+CGATAAAGTACAAAAGGGCACACCGCTTCTCGACCTGACCATTCCTGACTGGGTGGAAGC\n+GCAGAGTGAGTATTTACTGCTGCGCGAAACCGGCGGTACGGCGACCCAGACTGAAGGCAT\n+TCTTGAGCGGCTGCGACTGGCGGGAATGCCGGAGGCGGATATTCGCCGCCTGATCGCCAC\n+GCAAAAAATCCAGACTCGCTTTACGCTCAAAGCGCCCATTGATGGCGTGATCACCGCGTT\n+TGATCTGCGCGCGGGAATGAATATCGCCAAAGATAACGTGGTAGCGAAAATTCAGGGTAT\n+GGACCCGGTGTGGGTCACTGCTGCGATCCCGGAGTCTATCGCCTGGCTGGTGAAAGATGC\n+CTCGCAGTTTACCCTCACCGTTCCGGCGCGACCGGATAAAACACTCACCATCCGCAAATG\n+GACGCTGCTACCTGGCGTGGATGCCGCGACCCGCACGCTGCAGCTGCGTCTGGAAGTCGA\n+CAACGCCGACGAGGCGCTAAAACCGGGCATGAACGCCTGGTTGCAACTCAACACCGCCAG\n+CGAACCGATGCTGCTCATTCCGTCACAAGCGCTGATTGATACCGGCAGCGAACAGCGGGT\n+GATTACCGTTGATGCCGACGGGCGCTTTGTACCGAAACGCGTTGCTGTTTTCCAGGCATC\n+GCAAGGCGTCACCGCATTACGCTCTGGTCTGGCGGAAGGTGAAAAGGTGGTTTCCAGCGG\n+CCTGTTCCTGATTGATTCCGAAGCCAATATTTCTGGCGCACTGGAGCGGATGCGCTCTGA\n+AAGTGCTACCCATGCGCATTGAGGGAATAACCAATGATTGAATGGATTATTCGTCGCTCG\n+GTGGCGAACCGTTTTTTGGTGCTGATGGGCGCGTTGTTTCTGAGCATCTGGGGCACCTGG\n+ACCATCATTAATACGCCAGTGGATGCGCTGCCGGATCTCTCCGATGTGCAGGTTATTATT\n+AAAACCAGCTATCCCGGTCAGGCACCACAAATCGTTGAAAATCAGGTGACTTATCCGCTA\n+ACCACCACCATGTTGTCGGTGCCTGGCGCGAAGACTGTGCGCGGTTTCTCACAGTTTGGC\n+GACTCTTATGTGTATGTCATTTTCGAAGATGGCACCGATCCGTACTGGGCGCGTTCGCGG\n+GTGCTGGAGTACCTCAACCAGGTACAGGGTAAGCTGCCTGCGGGAGTCAGCGCCGAGCTG\n+GGGCCAGATGCCACGGGTGTTGGCTGGATCTATGAATATGCACTGGTGGATCGCAGCGGT\n+AAGCACGATCTGGCCGATTTACGCTCATTACAGGACTGGTTTCTCAAATATGAGCTGAAA\n+ACCATCCCTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTG\n+GTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCG\n+CTGGATGCTTCAAACCAGGAAGCGGGCGGTTCGTCGATCGAACTGGCGGAAGCGGAATAT\n+ATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAA\n+GCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCG\n+GAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTG\n+ATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAA\n+ACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAG\n+CTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTG\n+GCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCG\n+TTGCCGCTGGGGTTGTGTATTGCTTTTATTGTCATGCACTTCCAGGGACTGAATGCCAAT\n+ATTATGTCGTTGGGTGGCATTGCGATTGCCGTCGGGGCGATGGTCGATGCTGCTATCGTC\n' |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/test_02.genbank --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02.genbank Tue May 31 14:04:07 2022 +0000 |
| b |
| b'@@ -0,0 +1,182 @@\n+LOCUS ARBH01000003 3500 bp DNA linear BCT 22-APR-2013\n+DEFINITION Amycolatopsis balhimycina FH 1894 strain DSM 44591\n+ A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.\n+ACCESSION ARBH01000003\n+VERSION ARBH01000003.1\n+DBLINK BioProject: PRJNA165347\n+ BioSample: SAMN02256403\n+KEYWORDS WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.\n+SOURCE Amycolatopsis balhimycina FH 1894\n+ ORGANISM Amycolatopsis balhimycina FH 1894\n+ Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;\n+ Amycolatopsis.\n+REFERENCE 1 (bases 1 to 3500)\n+ AUTHORS Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N.,\n+ Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N.,\n+ Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N.,\n+ Hua,S.X. and Woyke,T.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell\n+ Drive, Walnut Creek, CA 94598-1698, USA\n+COMMENT ##MIGS-Data-START##\n+ investigation_type :: bacteria_archaea\n+ project_name :: Amycolatopsis balhimycina DSM 44591\n+ collection_date :: Missing\n+ lat_lon :: Missing\n+ depth :: Missing\n+ alt_elev :: Missing\n+ country :: India\n+ num_replicons :: Missing\n+ ref_biomaterial :: DSM 44591\n+ biotic_relationship :: Free living\n+ rel_to_oxygen :: Aerobe\n+ isol_growth_condt :: Missing\n+ assembly :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. 4.24\n+ finishing_strategy :: Missing\n+ environment :: Soil\n+ trophic_level :: Missing\n+ sequencing_meth :: WGS\n+ GOLD Stamp ID :: Gi10728\n+ Type Strain :: Yes\n+ Funding Program :: DOE-CSP 2011\n+ Isolation Site :: Soil\n+ Cell Shape :: Filament-shaped\n+ Motility :: Nonmotile\n+ Sporulation :: Sporulating\n+ Temperature Range :: Mesophile\n+ Gram Staining :: Gram+\n+ Diseases :: None\n+ ##MIGS-Data-END##\n+ ##Genome-Assembly-Data-START##\n+ Finishing Goal :: Improved High-Quality Draft\n+ Current Finishing Status :: Improved High-Quality Draft\n+ Assembly Method :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v.\n+ 4.24\n+ Genome Coverage :: Unknown\n+ Sequencing Technology :: Illumina GAii\n+ ##Genome-Assembly-Data-END##\n+ URL -- http://www.jgi.doe.gov\n+ JGI Project ID: 404843\n+ Source DNA and Organism available from Hans-Peter Klenk\n+ (hpk@dsmz.de)\n+ Source DNA available from Hans-Peter Klenk (hpk@dsmz.de)\n+ Organism available from Hans-Peter Klenk (hpk@dsmz.de)\n+ Contacts: Hans-Peter Klenk (hpk@dsmz.de)\n+ Tanja Woyke (microbe@cuba.jgi-psf.org)\n+ Whole genome sequencing and draft assembly at JGI-PGF\n+ Annotation by JGI-ORNL\n+ The JGI and collaborators endorse the principles for the\n+ distribution and use of large scale sequencing data adopted by the\n+ larger genome sequencing community and urge users of this data to\n+ follow them. It is our intention to publish the work of this\n+ project in a timely fashion and we welcome collaborative\n+ interaction on the project and analysis.\n+ (http://www.genome.gov/page.cfm?pageID=10506376)\n+ Full annotations a'..b'g cgcggttgcg ggccgagggc cggaccgtgc\n+ 421 ggaacgtggt gcacacggcc gccgtgatcg agctgcacac gctggccgag accgacctgg\n+ 481 ccgcgttctc ccggaccgtg cacgccaagg tggtgggcgc gcgcaacctg gacgagctgc\n+ 541 tcgacaccga cgagctcgat gcgttcgtgc tgtactcctc caccgccggc ctgtggggca\n+ 601 ccggcgcgca cgccgcctac gtggccggca acgcgtactt gcacgcgctg gcagcccacc\n+ 661 ggcgcgcccg ggggctgcgg gccaccgcgc tgtcgtgggg catctgggcc gacgaccgcg\n+ 721 aactcggccg ggtcgacccg gagcagatcg tgcgcagcgg cctggtgttc atggcgccgg\n+ 781 agctggcgct ggagggtctg cgccgggccc tggacgacga cgagaccgcg ctggccgtgg\n+ 841 ccgatctgga ctgggagcgg tactacccgg tctacaccgc cgtccggccg acgctgctgt\n+ 901 tcgacgagct gccggaggtg cggcggctca ccgaggccgc cgccgccacg gccgccaccg\n+ 961 gcgccggcgg cgagttcgcc gcccggctgc gcacgctgcc cgaggccgag cgcgcccacc\n+ 1021 tgctcctgga actggtccgg gccgaggccg cggccgtgct gggccacgcg tcggccgacg\n+ 1081 cgctgcccga ggaccgcgcc ttccgcgacg tcggcttcga ctcggtcacc gcggtcgacc\n+ 1141 tgcgcaaccg gatctccgcc ggcaccggcc tgaccctgcc cgccaccatg gtgttcgacc\n+ 1201 acccgacgcc gaggcggctg gccgggttcc tggccgccac gatcaccggc tcgggtgccg\n+ 1261 tcgagcaggc accggccgtg gccggcgtgg acaccggcga gcccgtcgcc atcatcggga\n+ 1321 tggcctgccg ctacccgggt ggcgcgaaca ccccggaacg gttgtgggac ctggtcgtgg\n+ 1381 gcggcgtgga cgccatctcc ggcttcccgg ccgaccgcaa ctggccgacc gacgcgctct\n+ 1441 acgacccgga cccggacgcc ggcggcaaga cctattcggt gcagggcggc ttcctgcacg\n+ 1501 aggcggccga gttcgacccg ggcttcttcg gcatctcgcc gcgggaggca ctgtccatgg\n+ 1561 atccgcagca gcgcctgctg ctggagacgg cgtgggaggc gttcgagcgg gccgggatcg\n+ 1621 acccgcacac gctgcggggc agcggcaccg gcaccttcat cggggccagc taccaggact\n+ 1681 acaccgcggc cgtgtccggc gcggtggaca acgccgacgg ccacatgatc accggctcgc\n+ 1741 tgggcagcat cctgtccggc cggctctcct acctgttcgg gctggagggc ccggcggtca\n+ 1801 ccctggacac cgcctgctcg tcgtcgctgg tcgccatcca cctggccgcg cagtcgctgc\n+ 1861 ggtcggggga gagcagcctg gcgctggccg gcggggtgag cgtgatggcg acgccggggg\n+ 1921 cgttcgtcgg cttctcgcgc cagcgcgcac tggccacgga cggccgttgc aaggcctact\n+ 1981 cggaccgggc cgacggcatg accctcggcg agggcgtcgg cctggtgctg ctggagaagc\n+ 2041 tgtccgacgc gcagcgcaac gggcaccgga tcctggcggt ggtccggggt tcggccacga\n+ 2101 accaggacgg cgcgtccaac ggcatgaccg cgcccagcgg cccgtcccag cagcgggtga\n+ 2161 tccggcaggc gctggccaac gcgcggctct cggcgtccga ggtggacgtg atcgagggcc\n+ 2221 acggcaccgg caccgcgctg ggcgacccga tcgaggccca ggccctgctg gccacctacg\n+ 2281 gccaggaccg ggaacggccg ctgctgctcg gctcggtgaa gtccaacatc ggccacaccc\n+ 2341 agatggcctc cggcgtggcc ggcgtgatca aggtggtgca ggcgctgcgg cacgggctgg\n+ 2401 tacccaagac gctgcacgtg gacgagccct ccacgcacgt cgactggagc accggctcga\n+ 2461 tcgagctgcc gtccggcagc gtgccgtggc cggagagcgg ccggccgcgc cgggccggta\n+ 2521 tctcgtcctt cgggctgagc ggcacgaacg tgcacaccat cctcgagcag gccccggaac\n+ 2581 cggccgccga agccggcccc gagccggagc ccggcctggt gccggtcccg ctgtccggcc\n+ 2641 ggacggaagc agcgctgcgc gctcaggccg ccaccgtgct ggacaccctg gacgacggcg\n+ 2701 tgtcgccggc cgtgctcggg tactcgctgg cctccacccg gtcggccttc gaacaccgtg\n+ 2761 cggtgctgct ggccgaggac cacgacgaac tgcggcgcgg cctggccgca ctggccggcg\n+ 2821 accagccgga cggcggcgtg gtgcggggca ccgtgacgcg gggccgcacg gcgttcctgt\n+ 2881 tcgccggcca gggcagccag cgggccggga tgggccgcga gctgtacgag cgccacccgg\n+ 2941 tgttcgccga cgcgctggac gcggtgctgg ggcacttcga cctgccccgt gcgctgcggg\n+ 3001 acgtgatgtg ggacgacgat tccacggccc tcgacgagac ggggtacacc cagccggcgt\n+ 3061 tgttcgcctt cgaggtggcg ttgttccggt tgctggagtc gtggggtgtg acgccggatt\n+ 3121 acctggccgg gcattcgatc ggtgagatcg ccgcggcgca cgtggccgga gtgttgtcgc\n+ 3181 tggccgatgc ctgtgcgttg gtcgctgcgc ggggtgcgct gatgcaggcg ctgccgtccg\n+ 3241 gcggggccat ggtttcggtg cgcggctccg aggccgacgt cgccgggcac ctcggcgagg\n+ 3301 acgtcgccgt cgcggcggtc aacgggcccg agtcggtggt gctggccggg accgaggacg\n+ 3361 cggtgctcca ggcggccggc cgcctggagg ccgccggcca caaggtccgc cgcctgcggg\n+ 3421 tcagccacgc cttccactcg cccttgatgg atcccgtgct ggccgagttc gcgacggtgg\n+ 3481 ctcagggcct gacctaccac\n+//\n' |
| b |
| diff -r 5784e268efca -r e78e25d3b4bd test-data/test_03.genbank --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.genbank Tue May 31 14:04:07 2022 +0000 |
| b |
| b'@@ -0,0 +1,23749 @@\n+LOCUS Chromosome 599940 bp DNA UNK 01-JAN-1980\n+DEFINITION Chromosome dna:chromosome chromosome:ASM584v2:Chromosome:1:4641652:1\n+ REF.\n+ACCESSION Chromosome\n+VERSION Chromosome\n+KEYWORDS .\n+SOURCE .\n+ ORGANISM .\n+ .\n+COMMENT ##antiSMASH-Data-START##\n+ Version :: 6.1.1\n+ Run date :: 2022-05-11 13:41:17\n+ ##antiSMASH-Data-END##\n+FEATURES Location/Qualifiers\n+ PFAM_domain 190..252\n+ /aSDomain="Leader_Thr"\n+ /aSTool="fullhmmer"\n+ /database="34.0"\n+ /db_xref="PF08254.13"\n+ /description="Threonine leader peptide"\n+ /detection="hmmscan"\n+ /domain_id="fullhmmer_thrL_0001"\n+ /evalue="5.80E-10"\n+ /label="thrL"\n+ /locus_tag="thrL"\n+ /protein_end="21"\n+ /protein_start="0"\n+ /score="38.8"\n+ /tool="antismash"\n+ /translation="MKRISTTITTTITITTGNGAG"\n+ mRNA 190..255\n+ /ID="transcript:AAC73112"\n+ /Name="thrL-1"\n+ /Parent="gene:b0001"\n+ /biotype="protein_coding"\n+ /gene="thrL"\n+ /source="ena"\n+ /transcript_id="AAC73112"\n+ exon 190..255\n+ /Name="AAC73112-1"\n+ /Parent="transcript:AAC73112"\n+ /constitutive="1"\n+ /ensembl_end_phase="0"\n+ /ensembl_phase="0"\n+ /exon_id="AAC73112-1"\n+ /gene="thrL"\n+ /rank="1"\n+ /source="ena"\n+ gene 190..255\n+ /ID="gene:b0001"\n+ /Name="thrL"\n+ /biotype="protein_coding"\n+ /description="thr operon leader peptide"\n+ /gene="gene189_255"\n+ /gene_id="b0001"\n+ /logic_name="ena"\n+ /source="ena"\n+ CDS 190..255\n+ /ID="CDS:AAC73112"\n+ /gene="thrL"\n+ /phase="0"\n+ /protein_id="AAC73112"\n+ /source="ena"\n+ /transl_table=11\n+ /translation="MKRISTTITTTITITTGNGAG"\n+ mRNA 337..2799\n+ /ID="transcript:AAC73113"\n+ /Name="thrA-1"\n+ /Parent="gene:b0002"\n+ /biotype="protein_coding"\n+ /gene="thrA"\n+ /source="ena"\n+ /transcript_id="AAC73113"\n+ exon 337..2799\n+ /Name="AAC73113-1"\n+ /Parent="transcript:AAC73113"\n+ /constitutive="1"\n+ /ensembl_end_phase="0"\n+ /ensembl_phase="0"\n+ /exon_id="AAC73113-1"\n+ /gene="thrA"\n+ /rank="1"\n+ /source="ena"\n+ gene 337..2799\n+ /ID="gene:b0002"\n+ /Name="thrA"\n+ /biotype="protein_coding"\n+ /description="fused aspartate kinase/homoserine\n+ dehydrogenase 1"\n+ /gene="gene336_2799"\n+ /gene_id="b0002"\n+ /logic_name="ena"\n+ /source="ena"\n+ CDS 337..2799\n+ /ID="CDS:AAC73113"\n+ /gene="thrA"\n+ /phase="0"\n+ /protein_id="AAC73113"\n+ /source="ena"\n+ '..b'1 gcgcgggcat tatatcagca cggcgcagta agttatctgg aagtgctgga tgccgagcgt\n+ 596881 tctttatttg caacccgaca aactttactt gatctgaatt atgcccgtca ggttaacgaa\n+ 596941 atttctttgt ataccgcact tggtggcggt tgacagcaat atactcgtca tacttcaagt\n+ 597001 tgcatgtgct gcgtctgcgt tcgctcaccc cagtcactta cttatgtaag ctcctgggga\n+ 597061 ttcactcgct tgtcgccttc ctgcaactcg aattatttag agtatgactt ttaactccag\n+ 597121 gagagaataa atgaaaaaag cactgcaagt cgcaatgttc agtctgttta ccgttattgg\n+ 597181 ctttaatgcc caggctaacg aacatcatca tgaaaccatg agcgaagcac aaccacaggt\n+ 597241 tattagcgcc actggcgtgg taaagggtat cgatctggaa agcaaaaaaa tcaccatcca\n+ 597301 tcacgatccg attgctgccg tgaactggcc ggagatgacc atgcgcttta ccatcacccc\n+ 597361 gcagacgaaa atgagtgaaa ttaaaaccgg cgacaaagtg gcgtttaatt ttgtccagca\n+ 597421 gggcaacctt tctttattac aggatattaa agtcagccag taacccaggt ttaatgagat\n+ 597481 gaaaaaaatc gcgcttatta tcggcagcat gatcgcgggc ggtattattt ctgcggcagg\n+ 597541 ttttacctgg gttgcaaagg cggaaccgcc tgcagaaaaa acgtcgaccg cagaacgtaa\n+ 597601 aatcttattc tggtacgacc caatgtatcc caatacgcgg ttcgataaac caggtaaatc\n+ 597661 gccgtttatg gatatggatc tggtgccgaa atatgccgat gaagagagtt ctgcgtctgg\n+ 597721 tgtgcgcatt gacccgactc agacgcagaa tctgggggtg aaaacggcta ccgtcacgcg\n+ 597781 cggaccgctg acttttgccc agagtttccc ggcgaatgtc agttacaacg agtatcagta\n+ 597841 tgccattgtg caggctcgcg ctgccgggtt tatcgacaag gtgtatccgc ttaccgtggg\n+ 597901 cgataaagta caaaagggca caccgcttct cgacctgacc attcctgact gggtggaagc\n+ 597961 gcagagtgag tatttactgc tgcgcgaaac cggcggtacg gcgacccaga ctgaaggcat\n+ 598021 tcttgagcgg ctgcgactgg cgggaatgcc ggaggcggat attcgccgcc tgatcgccac\n+ 598081 gcaaaaaatc cagactcgct ttacgctcaa agcgcccatt gatggcgtga tcaccgcgtt\n+ 598141 tgatctgcgc gcgggaatga atatcgccaa agataacgtg gtagcgaaaa ttcagggtat\n+ 598201 ggacccggtg tgggtcactg ctgcgatccc ggagtctatc gcctggctgg tgaaagatgc\n+ 598261 ctcgcagttt accctcaccg ttccggcgcg accggataaa acactcacca tccgcaaatg\n+ 598321 gacgctgcta cctggcgtgg atgccgcgac ccgcacgctg cagctgcgtc tggaagtcga\n+ 598381 caacgccgac gaggcgctaa aaccgggcat gaacgcctgg ttgcaactca acaccgccag\n+ 598441 cgaaccgatg ctgctcattc cgtcacaagc gctgattgat accggcagcg aacagcgggt\n+ 598501 gattaccgtt gatgccgacg ggcgctttgt accgaaacgc gttgctgttt tccaggcatc\n+ 598561 gcaaggcgtc accgcattac gctctggtct ggcggaaggt gaaaaggtgg tttccagcgg\n+ 598621 cctgttcctg attgattccg aagccaatat ttctggcgca ctggagcgga tgcgctctga\n+ 598681 aagtgctacc catgcgcatt gagggaataa ccaatgattg aatggattat tcgtcgctcg\n+ 598741 gtggcgaacc gttttttggt gctgatgggc gcgttgtttc tgagcatctg gggcacctgg\n+ 598801 accatcatta atacgccagt ggatgcgctg ccggatctct ccgatgtgca ggttattatt\n+ 598861 aaaaccagct atcccggtca ggcaccacaa atcgttgaaa atcaggtgac ttatccgcta\n+ 598921 accaccacca tgttgtcggt gcctggcgcg aagactgtgc gcggtttctc acagtttggc\n+ 598981 gactcttatg tgtatgtcat tttcgaagat ggcaccgatc cgtactgggc gcgttcgcgg\n+ 599041 gtgctggagt acctcaacca ggtacagggt aagctgcctg cgggagtcag cgccgagctg\n+ 599101 gggccagatg ccacgggtgt tggctggatc tatgaatatg cactggtgga tcgcagcggt\n+ 599161 aagcacgatc tggccgattt acgctcatta caggactggt ttctcaaata tgagctgaaa\n+ 599221 accatccctg acgttgcgga agtggcgtcg gtgggcggtg tggtgaaaga gtatcaggtg\n+ 599281 gttatcgatc cccagcgcct ggcgcagtat ggcatcagtc tcgccgaagt aaaaagcgcg\n+ 599341 ctggatgctt caaaccagga agcgggcggt tcgtcgatcg aactggcgga agcggaatat\n+ 599401 atggtgcgcg ccagcggcta tctgcaaacg ctcgacgact ttaatcacat cgttttaaaa\n+ 599461 gccagtgaaa atggcgtgcc cgtttatctg cgcgatgttg cgaaggtcca gattggcccg\n+ 599521 gagatgcgcc ggggcattgc cgaactaaac ggcgaaggcg aagtggcggg cggggtggtg\n+ 599581 atcctgcgat ccggcaaaaa cgcccgagaa gtgatcgccg ccgtgaagga caaactggaa\n+ 599641 acgctgaaaa gtagtctgcc ggaaggcgtg gagatagtta caacatacga tcgcagccag\n+ 599701 ctcattgacc gcgccatcga caacctcagc ggcaagttgc tggaagagtt tattgtggtg\n+ 599761 gcggtagtct gtgcgctgtt tctctggcat gtgcgctcgg cgctggtggc gattatttcg\n+ 599821 ttgccgctgg ggttgtgtat tgcttttatt gtcatgcact tccagggact gaatgccaat\n+ 599881 attatgtcgt tgggtggcat tgcgattgcc gtcggggcga tggtcgatgc tgctatcgtc\n+//\n' |