[med-svn] [tigr-glimmer] 01/01: Autopkgtest added

[Canberk Koç]

This is an automated email from the git hooks/post-receive script.

cbk-guest pushed a commit to branch master
in repository tigr-glimmer.

commit 089e7d84ade6094af8ff6cc8c04e9047fed36054
Author: cbk-guest <cbk-guests at scm.alioth.debian.org>
Date:   Fri Aug 12 07:33:39 2016 +0300

    Autopkgtest added
---
 debian/changelog                     |  6 ++++-
 debian/tests.tigr-glimmer/example.fa | 42 +++++++++++++++++++++++++++++++
 debian/tests/control                 |  3 +++
 debian/tests/run-unit-test           | 48 ++++++++++++++++++++++++++++++++++++
 debian/tigr-glimmer.examples         |  1 +
 5 files changed, 99 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index f53bd69..034928e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
 tigr-glimmer (3.02-5) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Moved packaging from SVN to Git
 
- -- Andreas Tille <tille at debian.org>  Thu, 11 Aug 2016 20:28:02 +0200
+  [ Canberk Koç ]
+  * Autopkgtest added
+
+ -- Canberk Koç <canberkkoc at gmail.com>  Fri, 12 Aug 2016 07:29:52 +0300
 
 tigr-glimmer (3.02-4) unstable; urgency=medium
 
diff --git a/debian/tests.tigr-glimmer/example.fa b/debian/tests.tigr-glimmer/example.fa
new file mode 100644
index 0000000..ff8aa63
--- /dev/null
+++ b/debian/tests.tigr-glimmer/example.fa
@@ -0,0 +1,42 @@
+>CALM_HUMAN
+MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD
+GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
+DEEVDEMIREADIDGDGQVNYEEFVQMMTAK
+>AF01595 Human telomerase reverse transcriptase (hTRT) mRNA
+MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCVP
+WDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTS
+VRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPLYQ
+LGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPK
+RPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRHS
+HPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPSL
+TGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTHC
+PLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLRRL
+VPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGCVPA
+AEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIGIR
+QHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRREK
+RAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPELYF
+VKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLT
+DLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYV
+QCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFLR
+TLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWCGLLLDTRTLEVQS
+DYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYK
+ILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAA
+GPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANP
+ALPSDFKTILD
+>P53_HUMAN
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
+DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
+SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
+RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
+SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGRDRRTEEENLRKKGEPHHELP
+PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
+GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>TUBE_DROME
+MAYGWNGCGMGVQVNGSNGAIGLSSKYSRNTELRRVEDNDIYRLAKILDENSCWRKLMS
+IIPKGMDVQACSGAGCLNFPAEIKKGFKYTAQDVFQIDEAANRLPPDQSKSQMMIDEWK
+TSGKLNERPTVGVLLQLLVQAELFSAADFVALDFLNESTPARPVDGPGALISLELLEEE
+MEVDNEGLSLKYQSSTATLGADAQGSVGLNLDNFEKDIVRRDKSVPQPSGNTPPIAPPR
+RQQRSTTNSNFATLTGTGTTSTTIPNVPNLTILNPSEQIQEPVLQPRPMNIPDLSILIS
+NSGDLRATVSDNPSNRTSSTDPPNIPRITLLIDNSGDVNSRPNHAPAKASTATTPTASS
+NNLPMISALNISKGSKETLRPESRSSSSSLSKDDDDDNDGEEDGEEEYPDAFLPNLSNS
+EQQSSNNDSSLTTVTGTSGDNSFELTNDSSSTSNDDYACNIPDLSELQQ
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..348566f
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,48 @@
+#!/bin/bash
+set -e
+
+pkg="tigr-glimmer"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+find . -name "*.gz" -exec gunzip \{\} \;
+
+echo "g3-from-scratch"
+echo "##################################"
+tigr-glimmer long-orfs -n -t 1.15 example.fa run1.longorfs
+tigr-glimmer extract -t example.fa run1.longorfs > run1.train
+tigr-glimmer build-icm -r run1.icm < run1.train
+tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run1.icm run1
+echo "=================================="
+
+# for making this test, need fasta file with coords
+#echo "g3-from-training"
+#echo "##################################"
+#tigr-glimmer extract -t example.fa train.coords > run2.train
+#tigr-glimmer build-icm -r run2.icm < run2.train
+#tigr-glimmer upstream-coords.awk 25 0 train.coords | extract example.fa - > run2.upstream
+##elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
+##set startuse = ‘start-codon-distrib -3 example.fa train.coords‘
+##tigr-glimmer glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse example.fa run2.icm run2
+
+echo "g3-iterated"
+echo "##################################"
+tigr-glimmer long-orfs -n -t 1.15 example.fa run3.longorfs
+tigr-glimmer extract -t example.fa run3.longorfs > run3.train
+tigr-glimmer build-icm -r run3.icm < run3.train
+tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run3.icm run3.run1
+tail -n+2 run3.run1.predict > run3.coords
+# for making full test, need elph (elph not in repo)
+#upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
+#elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
+#set startuse = ‘start-codon-distrib -3 genom.seq run3.coords‘
+#tigr-glimmer glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
+echo "=================================="
+
+echo "PASS"
diff --git a/debian/tigr-glimmer.examples b/debian/tigr-glimmer.examples
new file mode 100644
index 0000000..fedd71b
--- /dev/null
+++ b/debian/tigr-glimmer.examples
@@ -0,0 +1 @@
+debian/tests.tigr-glimmer/*

-- 
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