[med-svn] [progressivemauve] 01/01: add autopkgtest test-suite
Nadiya Sitdykova
rovenskasa-guest at moszumanska.debian.org
Thu Jul 13 22:37:50 UTC 2017
This is an automated email from the git hooks/post-receive script.
rovenskasa-guest pushed a commit to branch master
in repository progressivemauve.
commit af0a8cb269566e88195b0aecca6bdc947cb621be
Author: Nadiya Sitdykova <rovenskasa at 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 <rovenskasa at 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
+//
+
--
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