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commit af0a8cb269566e88195b0aecca6bdc947cb621be Author: Nadiya Sitdykova <rovensk...@gmail.com> Date: Thu Jul 13 18:37:14 2017 -0400 add autopkgtest test-suite --- debian/README.test | 8 +++ debian/changelog | 9 +++ debian/docs | 3 + debian/tests/control | 3 + debian/tests/run-unit-test | 31 +++++++++ debian/tests/test_data/all_virii.fasta | 102 ++++++++++++++++++++++++++++ debian/tests/test_data/genome_1.gbk | 116 ++++++++++++++++++++++++++++++++ debian/tests/test_data/genome_2.gbk | 116 ++++++++++++++++++++++++++++++++ debian/tests/test_data/genome_3.gbk | 117 +++++++++++++++++++++++++++++++++ 9 files changed, 505 insertions(+) diff --git a/debian/README.test b/debian/README.test new file mode 100644 index 0000000..39fbde9 --- /dev/null +++ b/debian/README.test @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by executing + + sh run-unit-test + +in order to confirm its integrity. diff --git a/debian/changelog b/debian/changelog index 884f9dd..9838143 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,12 @@ +progressivemauve (1.2.0+4713-3) UNRELEASED; urgency=medium + + * Team upload. + + [ Nadiya Sitdykova ] + * add autopkgtest test-suite + + -- Nadiya Sitdykova <rovensk...@gmail.com> Wed, 12 Jul 2017 21:53:52 -0400 + progressivemauve (1.2.0+4713-2) unstable; urgency=medium * Rebuild against gcc-5 ported libmems diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..d5a881e --- /dev/null +++ b/debian/docs @@ -0,0 +1,3 @@ +debian/README.test +debian/tests/run-unit-test +debian/tests/test_data diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..d2aa55a --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test new file mode 100644 index 0000000..6cb383a --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,31 @@ +#!/bin/sh -e + +pkg=progressivemauve + +if [ "$ADTTMP" = "" ] ; then + ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM +fi + +cd $ADTTMP + +cp -a /usr/share/doc/${pkg}/test_data/* . +gunzip -r * + +progressiveMauve --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --output=threeway.xmfa --output-guide-tree=threeway.tree --backbone-output=threeway.backbone genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --output=threeway_no_backbone.xmfa --disable-backbone genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --apply-backbone=threeway_no_backbone.xmfa --output=threeway.xmfa --backbone-output=threeway.backbone --hmm-p-go-homologous=0.001 --hmm-p-go-unrelated=0.000005 + +progressiveMauve --mums --output=threeway.mums genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --match-input=threeway.mums --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --output=threeway.xmfa --weight=50000 genome_1.gbk genome_2.gbk genome_3.gb + +progressiveMauve --min-scaled-penalty=5000 --output=threeway.xmfa genome_1.gbk genome_2.gbk genome_3.gbk + +progressiveMauve --collinear --seed-family --disable-backbone --output=virus.xmfa all_virii.fasta diff --git a/debian/tests/test_data/all_virii.fasta b/debian/tests/test_data/all_virii.fasta new file mode 100644 index 0000000..fc8ffb8 --- /dev/null +++ b/debian/tests/test_data/all_virii.fasta @@ -0,0 +1,102 @@ +>NC_025738.1 Faecal-associated gemycircularvirus 2, complete genome +TAATATTATACCCAGGACACAGGACACACCCCTCCTATAAATACCCCCCGCACCCCCCCTCGGCCGAACA +TGTCTCAAGAAATCACTCATGGCGTACGCACGCTCACGCGCAAAAAGGGGCACCGGTCGCTCAAAGAAGC +GTGGTGGACTCCGCCCACGCTATCGAAAGAAACGGCCAGCCTATCGCAAGAAGGGCGCCATGACCAAAAA +GCGGATCCTCAACCTGACCTCAACAAAAAAGCGAAACACTATGCTGCAGGTGGCGAACACTAGCTCGGTC +AATGGAGGACCAGTCACACCTGGACCCGGCCCATACGTCGTCAGCGACGTCAACGGCAGCCAATACAGTG +TCTTCATGCCCACCGCCCAGGATCTCAACGACAATAATGGTGCGGTCAACACTATCTCGAACCAAGCCCA +ACGAACTGCCACCACTTGTTTCATTAAGGGGTTCAACGAACGCATACGTATCCAAACCTCAAGTGGGATA +CCTTGGTTCTGGCGTCGCATATGCTTTCGCGCTAGGAATACCACCTTTTTCCTTTACTCCACCACCGACA +CGCCGTCTTCCACCACTGGCCCGGCCTATACCGAAACCAGCAATGGCATGCAGCGCCTCTACATGAATCT +CACTATCAACCAGTCAGGCCAGACTATTGGCAATATTCTTGGCGTATTGTTTCGTGGCCAAACTGGGATA +GATTGGGTGGACCCTCAGACCGCCTCGGTGGATACGACACGCGTCGACCTCGTATTCGATAAGCGCTACA +CCATCAAATCCGGTAACGCTAGTGGCACGGTCAGGGACTTTAACATTTGGCACCGCTATGGCAAGAACCT +GGTGTATGACGATGATGAGAACGGTAGTACGGAGGCTACTCGGTACAACTCGGTCAATGATAAGCGCGGT +GGCGGTGACCTTCTTATTTTTGATATCTTCACGCCCGGGACAGGTGCAGGCACTGCAGATCTTCTTCAGC +TGACTAGCACATCTACTCTGTATTGGCACGAAAAATAGCGTGATCTAGCTCCACAAAAATACAATTCCCG +TCCAACCATTTGATGTCTCCCTCGATTGCTGCCTGTTTACCCATGCTAGTGTGATTGGTGATTCCGTCGC +GGAGTTCCTCCCGAGGGTCCCGATTGCTCAGCCACACAACAGGCTTCCCCCAAGGCATCTGTACAGGATC +CCTGTACAACTTCTTCACTGTGACAACTGATTGGCACCCGAACCACTCCTTCCAGCCGTGGAAAAACTCT +AATCCTCCACGCATGTCATCGAACACAGCGTAGTCGGCGTCCGGCCCATCTCGCAACAGCACCTCACCTG +ACATCTGACCAATGGTGTAGATGTGGGGGCCAATGGAACGGGCCCACAGGGTCTTTCCCAATCTGGTATC +GCCGAAGATGACTAAGCTCTTAGCTCTTCCTAAACAAGTCAGCCTGATCCTTCGAAGTACAAACAAAGAT +GTATTCAGGCAACCGACGGGGGGGGGGATAGGGAGCCTGCGACCGAACCATTCCCCCCCCCTCGAGGGCG +GCAGTATGTTGCTTGTAACATACCTCGTTCCCGATCAACTCCAAGAGCGATATCTCTCCAGACAACCAAC +TCAGGTACATTTCCGAGCTCAAATTTGATCCCGGCGGGATGTTCATACTGAACAGGAGCGGGTCGATACT +TCCAGTTTGCATATGCTCGGAGACTCCCGTAATTGGTGCACAACGCCTTTGGATCCAGTCGTGCAACACA +TTCCCAAAACTCGCCCTCACTTTCTTGACTGACAATAATGCTCCACGAAGACACATCTTCGTAAACTCCT +CTTCCGCTCGGCCGAGGTAACCCTCCTGCGCAGACATCTCCATCCTTTGTCGCATAATCCCAGCCACCCT +CCGGCCTTCCGAAAGATGGCATGACGTTCGGGTGGCGGCCTCCAACATCAAAGACATCGGATCGTCGGGA +TCGAAACTTTCGGGAGAAATCGCAGAAAGCATGGAGATGAGTACCGTCATCAGCGTGCAACTCTCGTCCA +ATGATACACTCAGCTCCAAGGAATGACAGGTGGTCGTTAACGGCCCACGCATCAAGATCGCCGCACTGTG +CGTAGGTAAGGAGGACATAACGTGACTGAACAAAGTAGGCAGGTTTGGGTGGCATCGAAGTGTGTCCTGG +GAAAC + +>NC_025737.1 Faecal-associated gemycircularvirus 3, complete genome +TAATACTATACCCAGGACACAGGACACAGCACCCCCTATAAATACCCCCCTCACTCCCCCCCCTTCCTTA +TTTCAGAATGACACATCAAAATGGCCTACCGACGCAAGTCTTACTCATCACGGGTAAAAAGGCGAACCGG +GCGTACCGCGAGGCGTGGTGGACGCCGCCCAGCCTCCCAACAAAAGAGACGGACCTATCGCAAAAAGGGC +GCAATGTCGAAAAAGCGGATCCTCAATCTAACCAGCCGGAAGAAGCGGGACACCATGCTGACGTGGACCA +ACACGACCACCTCAGGCGGTCAAGTGTCGCCTAGGCCAGACGCCGCTTACGTCAAAGGTGATACCGGTGG +ATCCTTTTTGTGGGTTCCGACTGCTCGCGACCTCGTCGTAGGCAGCAACCTAGCCACGATTGCACTAGAG +AGTGCACGCACCTCGACCACGTGCTACATGCGCGGCCTATCGGAGAAGCTCCGCTTATCTACCTCGTCAG +GCGTCCCGTGGTTCCACCGCCGCATTTGTTTCACTTTCAAAGGCGCACAGCCCTTCCAATCAAACTTCAC +CGGCGATACCGGTTCCAATCAACTCTACCTGGAGAACTCCAACGGTTTAACGCGACTTATGTTCAATCAA +GCGGTGACAATACCCCCAAACTATCAGAATCAGATCAATTCCGTCATCTTCAAGGGCGCACAGGGTGTCG +ACTGGAGTGACGTCATCATTGCTCCCATTGATACTCGCCGTATCTCATTGAAGTACGATCGAACCTGGAC +CTACCGAAGCGGTAACGCTAATGGCACGGTCATGGAGAAGAAAATGTATCACCCGATGAACAAGAATATA +GTGTACGACGACGATGAGTCAGGGACCTCAGAGACAACGAGCTACTATTCGGTGGATTCTAAAGCCGGCA +TGGGAGACTATTACGTATGGGACATCTTCACAAGTGGACCCGGTGGAACCGCTACTGATCTGTTGAGATG +CGACATCTCATCTACTCTGTATTGGCACGAAAAATAGCGTGATCTAACTCCACAAAAATACAATTTCCGT +CCAACCATTTGATGTCCCCCTCAATTGATGCCTGTTTGCCCATGCTAGTGTGATTCGTAATGCTGTCACG +CAGCTCGTCCCGAGGATCACGATTGCTTAGCCAGATAACAGGCTTCCCCCAGGGCATCTGCACAGGATCC +CTGTACAACTTCTTGACTGTAACCACGGATTGACACCCAAACCACTCCTTCCAACCGTGGAAGAATTCCA +GTCCACCTCTCATGTCATCGAACACAGCGTAGTCGGCGTCTGGCCCATCCCTGAGGATGACCTCACCTGA +CATCTGACCAATAGTGTAGATGTGGGGGCCAATAGAACGAGCCCACAGGGTCTTTCCTAAACGGGTATCG +CCGAAGATGACTAAGCTCTTAGCTCTTCCTAAACAAGTTAGCACTACGCCACTATCCCTAGTAGAGATCT +GAAATAAGCGACCTCGAGACTCTAGCGGCGCACGAGGCCCCCCTCCGGGGGACGACGCCCGAGGCGGCGA +GGGGCCGTGCGCGCAAAGAGTCGACGGTCAAGACATACCTCGTTCCCGATCAGCTCCAAGAGCGATCTCT +CTCCAGACAGCCAACTCAGGTACCATTCCGAGCTCAAATTCGATCCCGGCGGGATGTTCGTACGGAACAG +GAGCGGGTCGGTAGCGCCAGTTCGCATATGCTCGGAGGCTGTTGTAATTGGTGCACAACGCACGTGGATC +CAGTCGTGCAACACACTTCCAAAACTCGCCCTCACTTTCTTGACCGACAATAATGCTCCACGAAGACACA +TCTTCGTAAACTCCTCTTCCGCTCGGCCGAGATAACCCTCCAGCGACCACGTCTCCATCTTTGATCGCAT +AGTCGTAACCGCCTTCCGGCTTTCCGTAAGATGGAACAAGGTTCGGGTGGCGGCCTCCAACATCAAAGAC +ATCGGATCGTCGGGATCGAAATCGGCGGGAGAAATCACAGAAAGCATGGAGATGAGTACCTCCATCAGCG +TGCAACTCTCGTCCAATGATACACTCAGCTCCAAGGAACGCCAAATGGTCATTAACGGTCCATGCATCAA +GAGTGCCGCACTGTGCGTACGTGAGAAGAAAGTATCGGCCATCGGCAAAATAGGGGTTAGGCTTGGCCTT +TGGTGGCATCGAAGAGTGTCCTGGGAAAC + +>NC_025736.1 Faecal-associated gemycircularvirus 4, complete genome +TAATGTTATAGCCAGAACACGGACTCACGAAGGGACCAACGTGTATAAATACCTCCCCTCCTCCCCCCAT +TATCGTTATCATGACACATCAAAATGGCTGCTCGCCGACTACCCCGCTCTCTCCCAACAGGACGCTACGG +CCGCGCAGGTCGCCGACGTGCTGCTCGTTATCCTCGAAAACGCCGCTCCACAGGCAGGAAGCGAACCTAT +CGCAAGCGAACTATGACTCGCAGGTCGATCCTCAACGTCACATCCGAGAAGAAGCGTGACAAAATGTTGC +AGATCACCAATTCCACTGCTGTCTCACAGTCCGGTAGTGGAACCTACCTTTCCCAATCCCGCAATTATTA +CCGGCGGCTCGTCTATGTCGCTGCATTCGTCTGGTGCGCCACCGCGCGTGACAACACCCGCAGCTCAACA +GCTACCCAACCCGGTAATAAGTTCGACGATAGCACCCGCACCGCGTCATCATGTTACATGGTGGGCTTGA +AGGAAACTATCGAATTACAGTGTCCCGACGGCCTCCCTTGGCAATGGCGTCGTATATGCGTCACTATGAA +GGGCACGGGCACCTTTGCTGGCACGCTAAACACTGGCACCTCAACATTTTACACCGCCCTCGAAACTAGC +AACGGCTTTTCCCGCGTCCTCAACCAAATCCTAGCCGCTGACCGCCTTTCCTTCTATGGTACCCTCTTTC +AAGGTCAACAGGATGTTGATTGGGCAGATCCTATGACTGCCAAGGTTGACAACGAACGACTTACAGTGAA +GTACGACAAAACTATCACACTTGCCTCTGGCAACGACGACGGTATGATCAGGAAGTATTCCAGGTATCAC +CGTATGGGCCACAACCTCGAGTACAACGATGACGAAAGTGGCGGTACCAAGACTGCCGGTCAGTTCTCAG +TCACTTCGAAGAAGGGTATGGGAGATTATTGGGTAATCGATTTATTCCGGCCTAGGGTCGGTTCTACAGC +TTCCAACCAGATGTTGTTCGGTACGGAGTCTACTCTGTATTGGCACGAAAGATAGCGTGGTCTAATTCCA +CAAAAATACAATTTCCGTCCAACCATTTGATGTCCCCCTCAATTGCTGCCTGTTTGCCAAGTGAAGTATG +ACACGTAATAGAATCGCGGAGTTCCTCCCTGGGATCCCGATTGGCCAACCAAATAACAGGCTTTCCCCAA +GGCATCTGCATGGGATCCTTGTACAACTTCTTGACAGTGACGACAGTCTGACAACCAAACCACTCCTTCC +AACCATGGAAGAAATCCAAACCACCCCTCATGTCATCGAATACAGCGTAATCGGCGTCGGGCCCATCCCT +GAGGATAACCTCACCTGACATCTGACCAATGGTGTAGATGTGGGGCCCAAGGGAACGTGCCCACAGGGTC +TTACCCAATCTAGTATCGCCGTAGATGACTAAGATCTTAGCTCTTCCTGCTTACGTAAGCAAATGATTAA +GCATAACATTTACCTTGCACGCGGTCGAGATTTGCTCGTGACCAGCTTGCCTGGTCCGAGCGCGAGACAC +GTGCGAAAGGCAACGCTCCTGCCAAATCAAACCCAGACAGAGATGTGAAATTGCACCCGAGCGGAGCGGA +CACTTACCTCGTTGCCGATTAGCTCCAAGAGCGATCTCTCTCCAGACAGCCAACTCAGGTACCATTCCGA +GCTCAAATTCGACCCCGGCGGGATGAACGTACTGAACAGGAGTGGGTCGATACTTCCAGTTCGCATATGC +TCGGAGGCTGTTGTAATTGGTGCACAACGAACGTGGATCCAGTCGTGCAACACATTCCCAAAAGTCCCCC +TCACTTTCTTGACTGACGATAATGCTCCACGAAGACACATCTTCGTAAACTCCTCTTCCGCCCGGCCGAG +ATAGCCCTCCAGCGACCACGTCTCCATCTTTGATCGCATAGTCATAACCGCCTTCCGGCCTTCCTCGAGA +TGCTTCAATGTTAGGGTGGAAGCCTCCAACATCAAACACATCGGGTCTTCGGGATCGAAACTTTCGGGAG +AAATCGCAGAAAGCATGGAGATGAGTACCCCCATCAGCGTGATGCTCTCGTCCAATGATACACTCACCGC +CAAGGAATGCCAGATGGTCATTAACGGCCCATGCATCAAGGTCGCCGCACTGTGCGTAGGTAAGGAGGAC +ATAGCGTGCTTGGAATTGAAATTGCTTGGGAGGCATGAAAGTGTTCTGGCAAAC + diff --git a/debian/tests/test_data/genome_1.gbk b/debian/tests/test_data/genome_1.gbk new file mode 100644 index 0000000..9797088 --- /dev/null +++ b/debian/tests/test_data/genome_1.gbk @@ -0,0 +1,116 @@ +LOCUS NC_025738 2175 bp DNA circular VRL 26-NOV-2014 +DEFINITION Faecal-associated gemycircularvirus 2, complete genome. +ACCESSION NC_025738 +VERSION NC_025738.1 +DBLINK BioProject: PRJNA268558 +KEYWORDS RefSeq. +SOURCE Faeces associated gemycircularvirus 2 + ORGANISM Faeces associated gemycircularvirus 2 + Viruses; Genomoviridae; Gemycircularvirus. +REFERENCE 1 (bases 1 to 2175) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L.M., Smalley,D., + Martin,D.P. and Varsani,A. + TITLE Novel myco-like DNA viruses discovered in the faecal matter of + various animals + JOURNAL Virus Res. 177 (2), 209-216 (2013) + PUBMED 23994297 +REFERENCE 2 (bases 1 to 2175) + CONSRTM NCBI Genome Project + TITLE Direct Submission + JOURNAL Submitted (26-NOV-2014) National Center for Biotechnology + Information, NIH, Bethesda, MD 20894, USA +REFERENCE 3 (bases 1 to 2175) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L., Smalley,D., + Roumagnac,P., Martin,D.P. and Varsani,A. + TITLE Direct Submission + JOURNAL Submitted (09-JUL-2013) School of Biological Sciences, University + of Canterbury, Private Bag 4800, Christchurch 8014, New Zealand +COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final + NCBI review. The reference sequence is identical to KF371640. + + ##Assembly-Data-START## + Assembly Method :: DNAMAN v. 7 + Sequencing Technology :: Sanger dideoxy sequencing + ##Assembly-Data-END## + COMPLETENESS: full length. +FEATURES Location/Qualifiers + source 1..2175 + /organism="Faeces associated gemycircularvirus 2" + /mol_type="genomic DNA" + /isolate="as5" + /isolation_source="feces" + /host="Sus scrofa" + /db_xref="taxon:1391031" + /country="New Zealand" + /collection_date="2011" + gene 89..1018 + /locus_tag="QU83_gp1" + /db_xref="GeneID:22284182" + CDS 89..1018 + /locus_tag="QU83_gp1" + /codon_start=1 + /product="capsid protein" + /protein_id="YP_009109734.1" + /db_xref="GeneID:22284182" + /translation="MAYARSRAKRGTGRSKKRGGLRPRYRKKRPAYRKKGAMTKKRIL + NLTSTKKRNTMLQVANTSSVNGGPVTPGPGPYVVSDVNGSQYSVFMPTAQDLNDNNGA + VNTISNQAQRTATTCFIKGFNERIRIQTSSGIPWFWRRICFRARNTTFFLYSTTDTPS + STTGPAYTETSNGMQRLYMNLTINQSGQTIGNILGVLFRGQTGIDWVDPQTASVDTTR + VDLVFDKRYTIKSGNASGTVRDFNIWHRYGKNLVYDDDENGSTEATRYNSVNDKRGGG + DLLIFDIFTPGTGAGTADLLQLTSTSTLYWHEK" + gene complement(993..2155) + /locus_tag="QU83_gp2" + /db_xref="GeneID:22284181" + CDS complement(join(993..1416,1560..2155)) + /locus_tag="QU83_gp2" + /codon_start=1 + /product="replication associated protein" + /protein_id="YP_009109735.1" + /db_xref="GeneID:22284181" + /translation="MPPKPAYFVQSRYVLLTYAQCGDLDAWAVNDHLSFLGAECIIGR + ELHADDGTHLHAFCDFSRKFRSRRSDVFDVGGRHPNVMPSFGRPEGGWDYATKDGDVC + AGGLPRPSGRGVYEDVSSWSIIVSQESEGEFWECVARLDPKALCTNYGSLRAYANWKY + RPAPVQYEHPAGIKFELGNVPELVVWRDIALGVDRERGILVIFGDTRLGKTLWARSIG + PHIYTIGQMSGEVLLRDGPDADYAVFDDMRGGLEFFHGWKEWFGCQSVVTVKKLYRDP + VQMPWGKPVVWLSNRDPREELRDGITNHTSMGKQAAIEGDIKWLDGNCIFVELDHAIF + RANTE" +ORIGIN + 1 taatattata cccaggacac aggacacacc cctcctataa ataccccccg caccccccct + 61 cggccgaaca tgtctcaaga aatcactcat ggcgtacgca cgctcacgcg caaaaagggg + 121 caccggtcgc tcaaagaagc gtggtggact ccgcccacgc tatcgaaaga aacggccagc + 181 ctatcgcaag aagggcgcca tgaccaaaaa gcggatcctc aacctgacct caacaaaaaa + 241 gcgaaacact atgctgcagg tggcgaacac tagctcggtc aatggaggac cagtcacacc + 301 tggacccggc ccatacgtcg tcagcgacgt caacggcagc caatacagtg tcttcatgcc + 361 caccgcccag gatctcaacg acaataatgg tgcggtcaac actatctcga accaagccca + 421 acgaactgcc accacttgtt tcattaaggg gttcaacgaa cgcatacgta tccaaacctc + 481 aagtgggata ccttggttct ggcgtcgcat atgctttcgc gctaggaata ccaccttttt + 541 cctttactcc accaccgaca cgccgtcttc caccactggc ccggcctata ccgaaaccag + 601 caatggcatg cagcgcctct acatgaatct cactatcaac cagtcaggcc agactattgg + 661 caatattctt ggcgtattgt ttcgtggcca aactgggata gattgggtgg accctcagac + 721 cgcctcggtg gatacgacac gcgtcgacct cgtattcgat aagcgctaca ccatcaaatc + 781 cggtaacgct agtggcacgg tcagggactt taacatttgg caccgctatg gcaagaacct + 841 ggtgtatgac gatgatgaga acggtagtac ggaggctact cggtacaact cggtcaatga + 901 taagcgcggt ggcggtgacc ttcttatttt tgatatcttc acgcccggga caggtgcagg + 961 cactgcagat cttcttcagc tgactagcac atctactctg tattggcacg aaaaatagcg + 1021 tgatctagct ccacaaaaat acaattcccg tccaaccatt tgatgtctcc ctcgattgct + 1081 gcctgtttac ccatgctagt gtgattggtg attccgtcgc ggagttcctc ccgagggtcc + 1141 cgattgctca gccacacaac aggcttcccc caaggcatct gtacaggatc cctgtacaac + 1201 ttcttcactg tgacaactga ttggcacccg aaccactcct tccagccgtg gaaaaactct + 1261 aatcctccac gcatgtcatc gaacacagcg tagtcggcgt ccggcccatc tcgcaacagc + 1321 acctcacctg acatctgacc aatggtgtag atgtgggggc caatggaacg ggcccacagg + 1381 gtctttccca atctggtatc gccgaagatg actaagctct tagctcttcc taaacaagtc + 1441 agcctgatcc ttcgaagtac aaacaaagat gtattcaggc aaccgacggg gggggggata + 1501 gggagcctgc gaccgaacca ttcccccccc ctcgagggcg gcagtatgtt gcttgtaaca + 1561 tacctcgttc ccgatcaact ccaagagcga tatctctcca gacaaccaac tcaggtacat + 1621 ttccgagctc aaatttgatc ccggcgggat gttcatactg aacaggagcg ggtcgatact + 1681 tccagtttgc atatgctcgg agactcccgt aattggtgca caacgccttt ggatccagtc + 1741 gtgcaacaca ttcccaaaac tcgccctcac tttcttgact gacaataatg ctccacgaag + 1801 acacatcttc gtaaactcct cttccgctcg gccgaggtaa ccctcctgcg cagacatctc + 1861 catcctttgt cgcataatcc cagccaccct ccggccttcc gaaagatggc atgacgttcg + 1921 ggtggcggcc tccaacatca aagacatcgg atcgtcggga tcgaaacttt cgggagaaat + 1981 cgcagaaagc atggagatga gtaccgtcat cagcgtgcaa ctctcgtcca atgatacact + 2041 cagctccaag gaatgacagg tggtcgttaa cggcccacgc atcaagatcg ccgcactgtg + 2101 cgtaggtaag gaggacataa cgtgactgaa caaagtaggc aggtttgggt ggcatcgaag + 2161 tgtgtcctgg gaaac +// + diff --git a/debian/tests/test_data/genome_2.gbk b/debian/tests/test_data/genome_2.gbk new file mode 100644 index 0000000..a5aa5bc --- /dev/null +++ b/debian/tests/test_data/genome_2.gbk @@ -0,0 +1,116 @@ +LOCUS NC_025737 2199 bp DNA circular VRL 26-NOV-2014 +DEFINITION Faecal-associated gemycircularvirus 3, complete genome. +ACCESSION NC_025737 +VERSION NC_025737.1 +DBLINK BioProject: PRJNA268557 +KEYWORDS RefSeq. +SOURCE Faeces associated gemycircularvirus 3 + ORGANISM Faeces associated gemycircularvirus 3 + Viruses; Genomoviridae; Gemycircularvirus. +REFERENCE 1 (bases 1 to 2199) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L.M., Smalley,D., + Martin,D.P. and Varsani,A. + TITLE Novel myco-like DNA viruses discovered in the faecal matter of + various animals + JOURNAL Virus Res. 177 (2), 209-216 (2013) + PUBMED 23994297 +REFERENCE 2 (bases 1 to 2199) + CONSRTM NCBI Genome Project + TITLE Direct Submission + JOURNAL Submitted (26-NOV-2014) National Center for Biotechnology + Information, NIH, Bethesda, MD 20894, USA +REFERENCE 3 (bases 1 to 2199) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L., Smalley,D., + Roumagnac,P., Martin,D.P. and Varsani,A. + TITLE Direct Submission + JOURNAL Submitted (09-JUL-2013) School of Biological Sciences, University + of Canterbury, Private Bag 4800, Christchurch 8014, New Zealand +COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final + NCBI review. The reference sequence is identical to KF371639. + + ##Assembly-Data-START## + Assembly Method :: DNAMAN v. 7 + Sequencing Technology :: Sanger dideoxy sequencing + ##Assembly-Data-END## + COMPLETENESS: full length. +FEATURES Location/Qualifiers + source 1..2199 + /organism="Faeces associated gemycircularvirus 3" + /mol_type="genomic DNA" + /isolate="P24c" + /isolation_source="feces" + /host="Gerygone albofrontata" + /db_xref="taxon:1391032" + /country="New Zealand" + /collection_date="2011" + gene 91..1017 + /locus_tag="QU82_gp1" + /db_xref="GeneID:22284179" + CDS 91..1017 + /locus_tag="QU82_gp1" + /codon_start=1 + /product="capsid protein" + /protein_id="YP_009109732.1" + /db_xref="GeneID:22284179" + /translation="MAYRRKSYSSRVKRRTGRTARRGGRRPASQQKRRTYRKKGAMSK + KRILNLTSRKKRDTMLTWTNTTTSGGQVSPRPDAAYVKGDTGGSFLWVPTARDLVVGS + NLATIALESARTSTTCYMRGLSEKLRLSTSSGVPWFHRRICFTFKGAQPFQSNFTGDT + GSNQLYLENSNGLTRLMFNQAVTIPPNYQNQINSVIFKGAQGVDWSDVIIAPIDTRRI + SLKYDRTWTYRSGNANGTVMEKKMYHPMNKNIVYDDDESGTSETTSYYSVDSKAGMGD + YYVWDIFTSGPGGTATDLLRCDISSTLYWHEK" + gene complement(992..2179) + /locus_tag="QU82_gp2" + /db_xref="GeneID:22284178" + CDS complement(join(992..1415,1575..2179)) + /locus_tag="QU82_gp2" + /codon_start=1 + /product="replication associated protein" + /protein_id="YP_009109733.1" + /db_xref="GeneID:22284178" + /translation="MPPKAKPNPYFADGRYFLLTYAQCGTLDAWTVNDHLAFLGAECI + IGRELHADGGTHLHAFCDFSRRFRSRRSDVFDVGGRHPNLVPSYGKPEGGYDYAIKDG + DVVAGGLSRPSGRGVYEDVSSWSIIVGQESEGEFWKCVARLDPRALCTNYNSLRAYAN + WRYRPAPVPYEHPAGIEFELGMVPELAVWREIALGADRERGILVIFGDTRLGKTLWAR + SIGPHIYTIGQMSGEVILRDGPDADYAVFDDMRGGLEFFHGWKEWFGCQSVVTVKKLY + RDPVQMPWGKPVIWLSNRDPRDELRDSITNHTSMGKQASIEGDIKWLDGNCIFVELDH + AIFRANTE" +ORIGIN + 1 taatactata cccaggacac aggacacagc accccctata aatacccccc tcactccccc + 61 cccttcctta tttcagaatg acacatcaaa atggcctacc gacgcaagtc ttactcatca + 121 cgggtaaaaa ggcgaaccgg gcgtaccgcg aggcgtggtg gacgccgccc agcctcccaa + 181 caaaagagac ggacctatcg caaaaagggc gcaatgtcga aaaagcggat cctcaatcta + 241 accagccgga agaagcggga caccatgctg acgtggacca acacgaccac ctcaggcggt + 301 caagtgtcgc ctaggccaga cgccgcttac gtcaaaggtg ataccggtgg atcctttttg + 361 tgggttccga ctgctcgcga cctcgtcgta ggcagcaacc tagccacgat tgcactagag + 421 agtgcacgca cctcgaccac gtgctacatg cgcggcctat cggagaagct ccgcttatct + 481 acctcgtcag gcgtcccgtg gttccaccgc cgcatttgtt tcactttcaa aggcgcacag + 541 cccttccaat caaacttcac cggcgatacc ggttccaatc aactctacct ggagaactcc + 601 aacggtttaa cgcgacttat gttcaatcaa gcggtgacaa tacccccaaa ctatcagaat + 661 cagatcaatt ccgtcatctt caagggcgca cagggtgtcg actggagtga cgtcatcatt + 721 gctcccattg atactcgccg tatctcattg aagtacgatc gaacctggac ctaccgaagc + 781 ggtaacgcta atggcacggt catggagaag aaaatgtatc acccgatgaa caagaatata + 841 gtgtacgacg acgatgagtc agggacctca gagacaacga gctactattc ggtggattct + 901 aaagccggca tgggagacta ttacgtatgg gacatcttca caagtggacc cggtggaacc + 961 gctactgatc tgttgagatg cgacatctca tctactctgt attggcacga aaaatagcgt + 1021 gatctaactc cacaaaaata caatttccgt ccaaccattt gatgtccccc tcaattgatg + 1081 cctgtttgcc catgctagtg tgattcgtaa tgctgtcacg cagctcgtcc cgaggatcac + 1141 gattgcttag ccagataaca ggcttccccc agggcatctg cacaggatcc ctgtacaact + 1201 tcttgactgt aaccacggat tgacacccaa accactcctt ccaaccgtgg aagaattcca + 1261 gtccacctct catgtcatcg aacacagcgt agtcggcgtc tggcccatcc ctgaggatga + 1321 cctcacctga catctgacca atagtgtaga tgtgggggcc aatagaacga gcccacaggg + 1381 tctttcctaa acgggtatcg ccgaagatga ctaagctctt agctcttcct aaacaagtta + 1441 gcactacgcc actatcccta gtagagatct gaaataagcg acctcgagac tctagcggcg + 1501 cacgaggccc ccctccgggg gacgacgccc gaggcggcga ggggccgtgc gcgcaaagag + 1561 tcgacggtca agacatacct cgttcccgat cagctccaag agcgatctct ctccagacag + 1621 ccaactcagg taccattccg agctcaaatt cgatcccggc gggatgttcg tacggaacag + 1681 gagcgggtcg gtagcgccag ttcgcatatg ctcggaggct gttgtaattg gtgcacaacg + 1741 cacgtggatc cagtcgtgca acacacttcc aaaactcgcc ctcactttct tgaccgacaa + 1801 taatgctcca cgaagacaca tcttcgtaaa ctcctcttcc gctcggccga gataaccctc + 1861 cagcgaccac gtctccatct ttgatcgcat agtcgtaacc gccttccggc tttccgtaag + 1921 atggaacaag gttcgggtgg cggcctccaa catcaaagac atcggatcgt cgggatcgaa + 1981 atcggcggga gaaatcacag aaagcatgga gatgagtacc tccatcagcg tgcaactctc + 2041 gtccaatgat acactcagct ccaaggaacg ccaaatggtc attaacggtc catgcatcaa + 2101 gagtgccgca ctgtgcgtac gtgagaagaa agtatcggcc atcggcaaaa taggggttag + 2161 gcttggcctt tggtggcatc gaagagtgtc ctgggaaac +// + diff --git a/debian/tests/test_data/genome_3.gbk b/debian/tests/test_data/genome_3.gbk new file mode 100644 index 0000000..273534d --- /dev/null +++ b/debian/tests/test_data/genome_3.gbk @@ -0,0 +1,117 @@ +LOCUS NC_025736 2224 bp DNA circular VRL 26-NOV-2014 +DEFINITION Faecal-associated gemycircularvirus 4, complete genome. +ACCESSION NC_025736 +VERSION NC_025736.1 +DBLINK BioProject: PRJNA268556 +KEYWORDS RefSeq. +SOURCE Faeces associated gemycircularvirus 4 + ORGANISM Faeces associated gemycircularvirus 4 + Viruses; Genomoviridae; Gemycircularvirus. +REFERENCE 1 (bases 1 to 2224) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L.M., Smalley,D., + Martin,D.P. and Varsani,A. + TITLE Novel myco-like DNA viruses discovered in the faecal matter of + various animals + JOURNAL Virus Res. 177 (2), 209-216 (2013) + PUBMED 23994297 +REFERENCE 2 (bases 1 to 2224) + CONSRTM NCBI Genome Project + TITLE Direct Submission + JOURNAL Submitted (26-NOV-2014) National Center for Biotechnology + Information, NIH, Bethesda, MD 20894, USA +REFERENCE 3 (bases 1 to 2224) + AUTHORS Sikorski,A., Massaro,M., Kraberger,S., Young,L., Smalley,D., + Roumagnac,P., Martin,D.P. and Varsani,A. + TITLE Direct Submission + JOURNAL Submitted (09-JUL-2013) School of Biological Sciences, University + of Canterbury, Private Bag 4800, Christchurch 8014, New Zealand +COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final + NCBI review. The reference sequence is identical to KF371638. + + ##Assembly-Data-START## + Assembly Method :: DNAMAN v. 7 + Sequencing Technology :: Sanger dideoxy sequencing + ##Assembly-Data-END## + COMPLETENESS: full length. +FEATURES Location/Qualifiers + source 1..2224 + /organism="Faeces associated gemycircularvirus 4" + /mol_type="genomic DNA" + /isolate="as50" + /isolation_source="feces" + /host="Arctocephalus forsteri" + /db_xref="taxon:1391033" + /country="New Zealand" + /collection_date="2012" + gene 94..1035 + /locus_tag="QU81_gp1" + /db_xref="GeneID:22284176" + CDS 94..1035 + /locus_tag="QU81_gp1" + /codon_start=1 + /product="capsid protein" + /protein_id="YP_009109730.1" + /db_xref="GeneID:22284176" + /translation="MAARRLPRSLPTGRYGRAGRRRAARYPRKRRSTGRKRTYRKRTM + TRRSILNVTSEKKRDKMLQITNSTAVSQSGSGTYLSQSRNYYRRLVYVAAFVWCATAR + DNTRSSTATQPGNKFDDSTRTASSCYMVGLKETIELQCPDGLPWQWRRICVTMKGTGT + FAGTLNTGTSTFYTALETSNGFSRVLNQILAADRLSFYGTLFQGQQDVDWADPMTAKV + DNERLTVKYDKTITLASGNDDGMIRKYSRYHRMGHNLEYNDDESGGTKTAGQFSVTSK + KGMGDYWVIDLFRPRVGSTASNQMLFGTESTLYWHER" + gene complement(1010..2206) + /locus_tag="QU81_gp2" + /db_xref="GeneID:22284175" + CDS complement(join(1010..1434,1615..2206)) + /locus_tag="QU81_gp2" + /codon_start=1 + /product="replication associated protein" + /protein_id="YP_009109731.1" + /db_xref="GeneID:22284175" + /translation="MPPKQFQFQARYVLLTYAQCGDLDAWAVNDHLAFLGGECIIGRE + HHADGGTHLHAFCDFSRKFRSRRPDVFDVGGFHPNIEASRGRPEGGYDYAIKDGDVVA + GGLSRPGGRGVYEDVSSWSIIVSQESEGDFWECVARLDPRSLCTNYNSLRAYANWKYR + PTPVQYVHPAGVEFELGMVPELAVWREIALGANRQRGILVIYGDTRLGKTLWARSLGP + HIYTIGQMSGEVILRDGPDADYAVFDDMRGGLDFFHGWKEWFGCQTVVTVKKLYKDPM + QMPWGKPVIWLANRDPREELRDSITCHTSLGKQAAIEGDIKWLDGNCIFVELDHAIFR + ANTE" +ORIGIN + 1 taatgttata gccagaacac ggactcacga agggaccaac gtgtataaat acctcccctc + 61 ctccccccat tatcgttatc atgacacatc aaaatggctg ctcgccgact accccgctct + 121 ctcccaacag gacgctacgg ccgcgcaggt cgccgacgtg ctgctcgtta tcctcgaaaa + 181 cgccgctcca caggcaggaa gcgaacctat cgcaagcgaa ctatgactcg caggtcgatc + 241 ctcaacgtca catccgagaa gaagcgtgac aaaatgttgc agatcaccaa ttccactgct + 301 gtctcacagt ccggtagtgg aacctacctt tcccaatccc gcaattatta ccggcggctc + 361 gtctatgtcg ctgcattcgt ctggtgcgcc accgcgcgtg acaacacccg cagctcaaca + 421 gctacccaac ccggtaataa gttcgacgat agcacccgca ccgcgtcatc atgttacatg + 481 gtgggcttga aggaaactat cgaattacag tgtcccgacg gcctcccttg gcaatggcgt + 541 cgtatatgcg tcactatgaa gggcacgggc acctttgctg gcacgctaaa cactggcacc + 601 tcaacatttt acaccgccct cgaaactagc aacggctttt cccgcgtcct caaccaaatc + 661 ctagccgctg accgcctttc cttctatggt accctctttc aaggtcaaca ggatgttgat + 721 tgggcagatc ctatgactgc caaggttgac aacgaacgac ttacagtgaa gtacgacaaa + 781 actatcacac ttgcctctgg caacgacgac ggtatgatca ggaagtattc caggtatcac + 841 cgtatgggcc acaacctcga gtacaacgat gacgaaagtg gcggtaccaa gactgccggt + 901 cagttctcag tcacttcgaa gaagggtatg ggagattatt gggtaatcga tttattccgg + 961 cctagggtcg gttctacagc ttccaaccag atgttgttcg gtacggagtc tactctgtat + 1021 tggcacgaaa gatagcgtgg tctaattcca caaaaataca atttccgtcc aaccatttga + 1081 tgtccccctc aattgctgcc tgtttgccaa gtgaagtatg acacgtaata gaatcgcgga + 1141 gttcctccct gggatcccga ttggccaacc aaataacagg ctttccccaa ggcatctgca + 1201 tgggatcctt gtacaacttc ttgacagtga cgacagtctg acaaccaaac cactccttcc + 1261 aaccatggaa gaaatccaaa ccacccctca tgtcatcgaa tacagcgtaa tcggcgtcgg + 1321 gcccatccct gaggataacc tcacctgaca tctgaccaat ggtgtagatg tggggcccaa + 1381 gggaacgtgc ccacagggtc ttacccaatc tagtatcgcc gtagatgact aagatcttag + 1441 ctcttcctgc ttacgtaagc aaatgattaa gcataacatt taccttgcac gcggtcgaga + 1501 tttgctcgtg accagcttgc ctggtccgag cgcgagacac gtgcgaaagg caacgctcct + 1561 gccaaatcaa acccagacag agatgtgaaa ttgcacccga gcggagcgga cacttacctc + 1621 gttgccgatt agctccaaga gcgatctctc tccagacagc caactcaggt accattccga + 1681 gctcaaattc gaccccggcg ggatgaacgt actgaacagg agtgggtcga tacttccagt + 1741 tcgcatatgc tcggaggctg ttgtaattgg tgcacaacga acgtggatcc agtcgtgcaa + 1801 cacattccca aaagtccccc tcactttctt gactgacgat aatgctccac gaagacacat + 1861 cttcgtaaac tcctcttccg cccggccgag atagccctcc agcgaccacg tctccatctt + 1921 tgatcgcata gtcataaccg ccttccggcc ttcctcgaga tgcttcaatg ttagggtgga + 1981 agcctccaac atcaaacaca tcgggtcttc gggatcgaaa ctttcgggag aaatcgcaga + 2041 aagcatggag atgagtaccc ccatcagcgt gatgctctcg tccaatgata cactcaccgc + 2101 caaggaatgc cagatggtca ttaacggccc atgcatcaag gtcgccgcac tgtgcgtagg + 2161 taaggaggac atagcgtgct tggaattgaa attgcttggg aggcatgaaa gtgttctggc + 2221 aaac +// + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/progressivemauve.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit