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diff test-data/test_02.genbank @ 4:e78e25d3b4bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit f5f8e44e726c9f2cc57e0f0fe8182a73afa56669
author bgruening
date Tue, 31 May 2022 14:04:07 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_02.genbank	Tue May 31 14:04:07 2022 +0000
@@ -0,0 +1,182 @@
+LOCUS       ARBH01000003            3500 bp    DNA     linear   BCT 22-APR-2013
+DEFINITION  Amycolatopsis balhimycina FH 1894 strain DSM 44591
+            A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.
+ACCESSION   ARBH01000003
+VERSION     ARBH01000003.1
+DBLINK      BioProject: PRJNA165347
+            BioSample: SAMN02256403
+KEYWORDS    WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.
+SOURCE      Amycolatopsis balhimycina FH 1894
+  ORGANISM  Amycolatopsis balhimycina FH 1894
+            Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
+            Amycolatopsis.
+REFERENCE   1  (bases 1 to 3500)
+  AUTHORS   Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N.,
+            Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N.,
+            Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N.,
+            Hua,S.X. and Woyke,T.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell
+            Drive, Walnut Creek, CA 94598-1698, USA
+COMMENT     ##MIGS-Data-START##
+            investigation_type       :: bacteria_archaea
+            project_name             :: Amycolatopsis balhimycina DSM 44591
+            collection_date          :: Missing
+            lat_lon                  :: Missing
+            depth                    :: Missing
+            alt_elev                 :: Missing
+            country                  :: India
+            num_replicons            :: Missing
+            ref_biomaterial          :: DSM 44591
+            biotic_relationship      :: Free living
+            rel_to_oxygen            :: Aerobe
+            isol_growth_condt        :: Missing
+            assembly :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v. 4.24
+            finishing_strategy       :: Missing
+            environment              :: Soil
+            trophic_level            :: Missing
+            sequencing_meth          :: WGS
+            GOLD Stamp ID            :: Gi10728
+            Type Strain              :: Yes
+            Funding Program          :: DOE-CSP 2011
+            Isolation Site           :: Soil
+            Cell Shape               :: Filament-shaped
+            Motility                 :: Nonmotile
+            Sporulation              :: Sporulating
+            Temperature Range        :: Mesophile
+            Gram Staining            :: Gram+
+            Diseases                 :: None
+            ##MIGS-Data-END##
+            ##Genome-Assembly-Data-START##
+            Finishing Goal           :: Improved High-Quality Draft
+            Current Finishing Status :: Improved High-Quality Draft
+            Assembly Method :: Velvet v. 1.1.05; ALLPATHS v. r38445; Phrap v.
+            4.24
+            Genome Coverage          :: Unknown
+            Sequencing Technology    :: Illumina GAii
+            ##Genome-Assembly-Data-END##
+            URL -- http://www.jgi.doe.gov
+            JGI Project ID: 404843
+            Source DNA and Organism available from Hans-Peter  Klenk
+            (hpk@dsmz.de)
+            Source DNA available from Hans-Peter  Klenk (hpk@dsmz.de)
+            Organism available from Hans-Peter  Klenk (hpk@dsmz.de)
+            Contacts: Hans-Peter  Klenk (hpk@dsmz.de)
+            Tanja Woyke (microbe@cuba.jgi-psf.org)
+            Whole genome sequencing and draft assembly at JGI-PGF
+            Annotation by JGI-ORNL
+            The JGI and collaborators endorse the principles for the
+            distribution and use of large scale sequencing data adopted by the
+            larger genome sequencing community and urge users of this data to
+            follow them. It is our intention to publish the work of this
+            project in a timely fashion and we welcome collaborative
+            interaction on the project and analysis.
+            (http://www.genome.gov/page.cfm?pageID=10506376)
+            Full annotations are available from IMG.
+            ##antiSMASH-Data-START##
+            Version      :: 6.1.1
+            Run date     :: 2022-05-11 13:39:18
+            ##antiSMASH-Data-END##
+FEATURES             Location/Qualifiers
+     source          1..3500
+                     /culture_collection="DSM:44591"
+                     /db_xref="taxon:1089545"
+                     /mol_type="genomic DNA"
+                     /organism="Amycolatopsis balhimycina FH 1894"
+                     /strain="DSM 44591"
+     CDS             complement(170..3134)
+                     /ID="input.cds1.1"
+                     /Name="input.path1.gene1"
+                     /Note="initial-exon"
+                     /gene="input.path1.gene1"
+                     /phase="0"
+                     /source="GlimmerHMM"
+                     /transl_table=1
+                     /translation="MPGQVIRRHTPRLQQPEQRHLEGEQRRLGVPRLVEGRGIVVPHHV
+                     PQRTGQVEVPQHRVQRVGEHRVALVQLAAHPGPLAALAGEQERRAAPRHGAPHHAAVRL
+                     VAGQCGQAAPQFVVVLGQQHRTVFEGRPGGGQRVPEHGRRHAVVQGVQHGGGLSAQRCF
+                     RPAGQRDRHQAGLRLGAGFGGRFRGLLEDGVHVRAAQPEGRDTGPARPAALRPRHAAGR
+                     QLDRAGAPVDVRGGLVHVQRLGYQPVPQRLHHLDHAGHAGGHLGVADVGLHRAEQQRPF
+                     PVLAVGGQQGLGLDRVAQRGAGAVALDHVHLGRREPRVGQRLPDHPLLGRAAGRGHAVG
+                     RAVLVRGRTPDHRQDPVPVALRVGQLLQQHQADALAEGHAVGPVRVGLATAVRGQCALA
+                     READERPRRRHHAHPAGQRQAALPRPQRLRGQVDGDQRRRAGGVQGDRRALQPEQVGEP
+                     AGQDAAQRAGDHVAVGVVHRAGHGRGVVLVAGPDEGAGAAAPQRVRVDPGPLERLPRRL
+                     QQQALLRIHGQCLPRRDAEEARVELGRLVQEAALHRIGLAAGVRVRVVERVGRPVAVGR
+                     EAGDGVHAAHDQVPQPFRGVRATRVAAGHPDDGDGLAGVHAGHGRCLLDGTRAGDRGGQ
+                     EPGQPPRRRVVEHHGGGQGQAGAGGDPVAQVDRGDRVEADVAEGAVLGQRVGRRVAQHG
+                     RGLGPDQFQEQVGALGLGQRAQPGGELAAGAGGGRGGGGLGEPPHLRQLVEQQRRPDGG
+                     VDRVVPLPVQIGHGQRGLVVVQGPAQTLQRQLRRHEHQAAAHDLLRVDPAEFAVVGPDA
+                     PRQRGGPQPPGAPVGCQRVQVRVAGHVGGVRAGAPQAGGGGVQHERIELVGVEQLVQVA
+                     RAHHLGVHGPGERGQVGLGQRVQLDHGGRVHHVPHGPALGPQPRQQGGQRRLVGDVAGH
+                     RLDGLAQLRQQLPGLRGLGAGAAGQHDVLGALLGQPAGQVRGQGAGAAGDQRGAARGP"
+     CDS             3249..3404
+                     /ID="input.cds2.1"
+                     /Name="input.path1.gene2"
+                     /Note="initial-exon"
+                     /gene="input.path1.gene2"
+                     /phase="0"
+                     /source="GlimmerHMM"
+                     /transl_table=1
+                     /translation="MVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAVLQAAGR
+                     LEAAGHK"
+ORIGIN
+        1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg
+       61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg
+      121 gccgccgcgt ggtgcgggcc ccggccggcg accgcgcgcc ggcgcggacc tggaccccgc
+      181 gcggcaccac gctgatcacc ggcggcaccg gcaccctggc cccgcacctg gcccgctggc
+      241 tggccgagca gggcgccgag cacatcgtgc tgaccagccg caccggcgcc gaggccccga
+      301 aggcccggca gctgctggcg gagctgggcg agaccgtcga ggcggtggcc tgcgacgtca
+      361 ccgacaaggc ggcgctggcc gccctgctgg cgcggttgcg ggccgagggc cggaccgtgc
+      421 ggaacgtggt gcacacggcc gccgtgatcg agctgcacac gctggccgag accgacctgg
+      481 ccgcgttctc ccggaccgtg cacgccaagg tggtgggcgc gcgcaacctg gacgagctgc
+      541 tcgacaccga cgagctcgat gcgttcgtgc tgtactcctc caccgccggc ctgtggggca
+      601 ccggcgcgca cgccgcctac gtggccggca acgcgtactt gcacgcgctg gcagcccacc
+      661 ggcgcgcccg ggggctgcgg gccaccgcgc tgtcgtgggg catctgggcc gacgaccgcg
+      721 aactcggccg ggtcgacccg gagcagatcg tgcgcagcgg cctggtgttc atggcgccgg
+      781 agctggcgct ggagggtctg cgccgggccc tggacgacga cgagaccgcg ctggccgtgg
+      841 ccgatctgga ctgggagcgg tactacccgg tctacaccgc cgtccggccg acgctgctgt
+      901 tcgacgagct gccggaggtg cggcggctca ccgaggccgc cgccgccacg gccgccaccg
+      961 gcgccggcgg cgagttcgcc gcccggctgc gcacgctgcc cgaggccgag cgcgcccacc
+     1021 tgctcctgga actggtccgg gccgaggccg cggccgtgct gggccacgcg tcggccgacg
+     1081 cgctgcccga ggaccgcgcc ttccgcgacg tcggcttcga ctcggtcacc gcggtcgacc
+     1141 tgcgcaaccg gatctccgcc ggcaccggcc tgaccctgcc cgccaccatg gtgttcgacc
+     1201 acccgacgcc gaggcggctg gccgggttcc tggccgccac gatcaccggc tcgggtgccg
+     1261 tcgagcaggc accggccgtg gccggcgtgg acaccggcga gcccgtcgcc atcatcggga
+     1321 tggcctgccg ctacccgggt ggcgcgaaca ccccggaacg gttgtgggac ctggtcgtgg
+     1381 gcggcgtgga cgccatctcc ggcttcccgg ccgaccgcaa ctggccgacc gacgcgctct
+     1441 acgacccgga cccggacgcc ggcggcaaga cctattcggt gcagggcggc ttcctgcacg
+     1501 aggcggccga gttcgacccg ggcttcttcg gcatctcgcc gcgggaggca ctgtccatgg
+     1561 atccgcagca gcgcctgctg ctggagacgg cgtgggaggc gttcgagcgg gccgggatcg
+     1621 acccgcacac gctgcggggc agcggcaccg gcaccttcat cggggccagc taccaggact
+     1681 acaccgcggc cgtgtccggc gcggtggaca acgccgacgg ccacatgatc accggctcgc
+     1741 tgggcagcat cctgtccggc cggctctcct acctgttcgg gctggagggc ccggcggtca
+     1801 ccctggacac cgcctgctcg tcgtcgctgg tcgccatcca cctggccgcg cagtcgctgc
+     1861 ggtcggggga gagcagcctg gcgctggccg gcggggtgag cgtgatggcg acgccggggg
+     1921 cgttcgtcgg cttctcgcgc cagcgcgcac tggccacgga cggccgttgc aaggcctact
+     1981 cggaccgggc cgacggcatg accctcggcg agggcgtcgg cctggtgctg ctggagaagc
+     2041 tgtccgacgc gcagcgcaac gggcaccgga tcctggcggt ggtccggggt tcggccacga
+     2101 accaggacgg cgcgtccaac ggcatgaccg cgcccagcgg cccgtcccag cagcgggtga
+     2161 tccggcaggc gctggccaac gcgcggctct cggcgtccga ggtggacgtg atcgagggcc
+     2221 acggcaccgg caccgcgctg ggcgacccga tcgaggccca ggccctgctg gccacctacg
+     2281 gccaggaccg ggaacggccg ctgctgctcg gctcggtgaa gtccaacatc ggccacaccc
+     2341 agatggcctc cggcgtggcc ggcgtgatca aggtggtgca ggcgctgcgg cacgggctgg
+     2401 tacccaagac gctgcacgtg gacgagccct ccacgcacgt cgactggagc accggctcga
+     2461 tcgagctgcc gtccggcagc gtgccgtggc cggagagcgg ccggccgcgc cgggccggta
+     2521 tctcgtcctt cgggctgagc ggcacgaacg tgcacaccat cctcgagcag gccccggaac
+     2581 cggccgccga agccggcccc gagccggagc ccggcctggt gccggtcccg ctgtccggcc
+     2641 ggacggaagc agcgctgcgc gctcaggccg ccaccgtgct ggacaccctg gacgacggcg
+     2701 tgtcgccggc cgtgctcggg tactcgctgg cctccacccg gtcggccttc gaacaccgtg
+     2761 cggtgctgct ggccgaggac cacgacgaac tgcggcgcgg cctggccgca ctggccggcg
+     2821 accagccgga cggcggcgtg gtgcggggca ccgtgacgcg gggccgcacg gcgttcctgt
+     2881 tcgccggcca gggcagccag cgggccggga tgggccgcga gctgtacgag cgccacccgg
+     2941 tgttcgccga cgcgctggac gcggtgctgg ggcacttcga cctgccccgt gcgctgcggg
+     3001 acgtgatgtg ggacgacgat tccacggccc tcgacgagac ggggtacacc cagccggcgt
+     3061 tgttcgcctt cgaggtggcg ttgttccggt tgctggagtc gtggggtgtg acgccggatt
+     3121 acctggccgg gcattcgatc ggtgagatcg ccgcggcgca cgtggccgga gtgttgtcgc
+     3181 tggccgatgc ctgtgcgttg gtcgctgcgc ggggtgcgct gatgcaggcg ctgccgtccg
+     3241 gcggggccat ggtttcggtg cgcggctccg aggccgacgt cgccgggcac ctcggcgagg
+     3301 acgtcgccgt cgcggcggtc aacgggcccg agtcggtggt gctggccggg accgaggacg
+     3361 cggtgctcca ggcggccggc cgcctggagg ccgccggcca caaggtccgc cgcctgcggg
+     3421 tcagccacgc cttccactcg cccttgatgg atcccgtgct ggccgagttc gcgacggtgg
+     3481 ctcagggcct gacctaccac
+//