[med-svn] r23881 - in trunk/packages/poa/trunk/debian: . tests tests/test_data
Nadiya Sitdykova
rovenskasa-guest at moszumanska.debian.org
Fri Jul 21 01:07:38 UTC 2017
Author: rovenskasa-guest
Date: 2017-07-21 01:07:36 +0000 (Fri, 21 Jul 2017)
New Revision: 23881
Added:
trunk/packages/poa/trunk/debian/README.test
trunk/packages/poa/trunk/debian/tests/
trunk/packages/poa/trunk/debian/tests/control
trunk/packages/poa/trunk/debian/tests/run-unit-test
trunk/packages/poa/trunk/debian/tests/test_data/
trunk/packages/poa/trunk/debian/tests/test_data/blosum80.mat
trunk/packages/poa/trunk/debian/tests/test_data/clustal.out
trunk/packages/poa/trunk/debian/tests/test_data/test1.fa
trunk/packages/poa/trunk/debian/tests/test_data/test2.fa
trunk/packages/poa/trunk/debian/tests/test_data/test3.fa
trunk/packages/poa/trunk/debian/tests/test_data/test4.fa
trunk/packages/poa/trunk/debian/tests/test_data/test5.fa
Modified:
trunk/packages/poa/trunk/debian/changelog
trunk/packages/poa/trunk/debian/docs
Log:
add autopkgtest test-suite
Added: trunk/packages/poa/trunk/debian/README.test
===================================================================
--- trunk/packages/poa/trunk/debian/README.test (rev 0)
+++ trunk/packages/poa/trunk/debian/README.test 2017-07-21 01:07:36 UTC (rev 23881)
@@ -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.
Modified: trunk/packages/poa/trunk/debian/changelog
===================================================================
--- trunk/packages/poa/trunk/debian/changelog 2017-07-20 11:45:30 UTC (rev 23880)
+++ trunk/packages/poa/trunk/debian/changelog 2017-07-21 01:07:36 UTC (rev 23881)
@@ -1,3 +1,12 @@
+poa (2.0+20060928-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+
+ [ Nadiya Sitdykova ]
+ * add autopkgtest test-suite
+
+ -- Nadiya Sitdykova <rovenskasa at gmail.com> Thu, 20 Jul 2017 21:04:02 -0400
+
poa (2.0+20060928-4) unstable; urgency=medium
* moved debian/upstream to debian/upstream/metadata
Modified: trunk/packages/poa/trunk/debian/docs
===================================================================
--- trunk/packages/poa/trunk/debian/docs 2017-07-20 11:45:30 UTC (rev 23880)
+++ trunk/packages/poa/trunk/debian/docs 2017-07-21 01:07:36 UTC (rev 23881)
@@ -1 +1,4 @@
README
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/test_data
Added: trunk/packages/poa/trunk/debian/tests/control
===================================================================
--- trunk/packages/poa/trunk/debian/tests/control (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/control 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
Added: trunk/packages/poa/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/poa/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/run-unit-test 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,25 @@
+#!/bin/sh -e
+
+pkg=poa
+
+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 *
+
+poa -read_fasta test1.fa -clustal clustal.aln blosum80.mat
+
+poa -read_msa clustal.aln -pir pir.aln blosum80.mat
+
+poa -read_fasta test2.fa -pir pir.aln -best blosum80.mat
+
+poa -read_fasta test3.fa -po po.aln blosum80.mat
+
+poa -read_fasta test4.fa -do_global -clustal clustal.aln blosum80.mat
+
+poa -read_fasta test5.fa -do_progressive -clustal clustal.aln blosum80.mat
Added: trunk/packages/poa/trunk/debian/tests/test_data/blosum80.mat
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/blosum80.mat (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/blosum80.mat 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM80 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -6
+R -2 6 -1 -2 -4 1 -1 -3 0 -3 -3 2 -2 -4 -2 -1 -1 -4 -3 -3 -1 -3 0 -1 -6
+N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -4 5 -4 0 -1 -6
+D -2 -2 1 6 -4 -1 1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4 5 -5 1 -1 -6
+C -1 -4 -3 -4 9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -2 -4 -1 -6
+Q -1 1 0 -1 -4 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -3 -2 -3 0 -3 4 -1 -6
+E -1 -1 -1 1 -5 2 6 -3 0 -4 -4 1 -2 -4 -2 0 -1 -4 -3 -3 1 -4 5 -1 -6
+G 0 -3 -1 -2 -4 -2 -3 6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -5 -3 -1 -6
+H -2 0 0 -2 -4 1 0 -3 8 -4 -3 -1 -2 -2 -3 -1 -2 -3 2 -4 -1 -4 0 -1 -6
+I -2 -3 -4 -4 -2 -3 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -4 3 -4 -1 -6
+L -2 -3 -4 -5 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -2 1 -4 3 -3 -1 -6
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 -1 -1 -4 -3 -3 -1 -3 1 -1 -6
+M -1 -2 -3 -4 -2 0 -2 -4 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 2 -1 -1 -6
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 0 6 -4 -3 -2 0 3 -1 -4 0 -4 -1 -6
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4 8 -1 -2 -5 -4 -3 -2 -4 -2 -1 -6
+S 1 -1 0 -1 -2 0 0 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -3 0 -1 -6
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2 1 5 -4 -2 0 -1 -1 -1 -1 -6
+W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2 0 -5 -4 -4 11 2 -3 -5 -3 -3 -1 -6
+Y -2 -3 -3 -4 -3 -2 -3 -4 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -3 -2 -3 -1 -6
+V 0 -3 -4 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 2 -3 -1 -6
+B -2 -1 5 5 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 5 -4 0 -1 -6
+J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 3 -3 2 0 -4 -3 -1 -3 -2 2 -4 3 -3 -1 -6
+Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -1 -4 -2 0 -1 -3 -3 -3 0 -3 5 -1 -6
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
Added: trunk/packages/poa/trunk/debian/tests/test_data/clustal.out
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/clustal.out (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/clustal.out 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,55 @@
+CLUSTAL W (1.74) multiple sequence alignment
+
+
+seq1 -------------------------------TGTACNTG-TTTGTG-AGG
+seq2 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq3 -A-GT--TCCTGC-TGCGTTTGCTGGACTTATGTACTTG-TTTGTG-AGG
+seq4 AA-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTGGTTTGTGNAGG
+seq5 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTN-AGG
+seq6 -A-GT--TCCTGC-TGCGTTTGCT--------------------------
+seq7 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTT-------
+seq8 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq9 -A-GT--TNCTGN-TGNGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq10 --------------------------------GTACNTG-TTTGTG-AGG
+seq11 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq12 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq13 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq14 -A-GT--TCCTGC-TGCTTTTGCTGGACTGATGTACTTG-ATTGTG-AGG
+seq15 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq16 -A-GT--TCCTGC-TGCGCTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq17 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-CGG
+seq18 -----AGTCCTGC--GCGTTTGC-GGACGGATGTACTTG-TT-GTG-AGG
+seq19 -------------------------------------------------G
+seq20 ------------------------------------------------GG
+seq21 ---------------------------CTGATGTACTTG-TT-GTGAGGG
+seq22 -A-GT--TCCTGC-TGCGTTTGCTGGACTGATGTACTTG-TTTGTG-AGG
+seq23 ------GTTCTGCCTGCGTTTGCTGAACTGATGTACTTG-TTAGTA-AG-
+seq24 --CGT--TACTGC-GGGGTTTGCTGGACTCATG-ACTTTGTTNGTA-GG-
+
+
+seq1 CTA
+seq2 CAA
+seq3 CAA
+seq4 CAA
+seq5 CAA
+seq6 ---
+seq7 ---
+seq8 CAA
+seq9 CAA
+seq10 CTA
+seq11 CAA
+seq12 CAA
+seq13 CAA
+seq14 CAA
+seq15 CAA
+seq16 CAA
+seq17 CAA
+seq18 CAA
+seq19 CAA
+seq20 CAA
+seq21 CAA
+seq22 CAA
+seq23 CAA
+seq24 CAA
+
+
Added: trunk/packages/poa/trunk/debian/tests/test_data/test1.fa
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/test1.fa (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/test1.fa 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,4 @@
+>seq1
+PKMIVRPQKNETV
+>seq2
+THKMLVRNETIM
Added: trunk/packages/poa/trunk/debian/tests/test_data/test2.fa
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/test2.fa (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/test2.fa 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,10 @@
+>seq1
+GAFTGEVSLPILKDFGVNWIVLGHSERRAYYGNEIVADKVAAAV
+>seq2
+GLASLKDFGVNWIVLGHSERRWYYGEVADKVAAAV
+>seq3
+GAFTGENSVDQIKDVGAKWVILGHSERRSEDDKFIADKTKFAL
+>seq4
+QAYTVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAF
+>seq5
+GSHTGHVLPEAVKEAGAVGTLLNHSENRMILADLEAAIRRAE
Added: trunk/packages/poa/trunk/debian/tests/test_data/test3.fa
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/test3.fa (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/test3.fa 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,10 @@
+>seq1
+PESLLYGRFTIESDVW
+>seq2
+PEAALYGRFTIKSDVW
+>seq3
+PESLAYNKFSIKSDVW
+>seq4
+PEALNYGRYSSESDVW
+>seq5
+PEVIRMQDDNPFSFQSDVY
Added: trunk/packages/poa/trunk/debian/tests/test_data/test4.fa
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/test4.fa (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/test4.fa 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,48 @@
+>seq1
+TGTACNTGTTTGTGAGGCTA
+>seq2
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq3
+AGTTCCTGCTGCGTTTGCTGGACTTATGTACTTGTTTGTGAGGCAA
+>seq4
+AAGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGGTTTGTGNAGGCAA
+>seq5
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTNAGGCAA
+>seq6
+AGTTCCTGCTGCGTTTGCT
+>seq7
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTT
+>seq8
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq9
+AGTTNCTGNTGNGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq10
+GTACNTGTTTGTGAGGCTA
+>seq11
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq12
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq13
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq14
+AGTTCCTGCTGCTTTTGCTGGACTGATGTACTTGATTGTGAGGCAA
+>seq15
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq16
+AGTTCCTGCTGCGCTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq17
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGCGGCAA
+>seq18
+AGTCCTGCGCGTTTGCGGACGGATGTACTTGTTGTGAGGCAA
+>seq19
+GCAA
+>seq20
+GGCAA
+>seq21
+CTGATGTACTTGTTGTGAGGGCAA
+>seq22
+AGTTCCTGCTGCGTTTGCTGGACTGATGTACTTGTTTGTGAGGCAA
+>seq23
+GTTCTGCCTGCGTTTGCTGAACTGATGTACTTGTTAGTAAGCAA
+>seq24
+CGTTACTGCGGGGTTTGCTGGACTCATGACTTTGTTNGTAGGCAA
Added: trunk/packages/poa/trunk/debian/tests/test_data/test5.fa
===================================================================
--- trunk/packages/poa/trunk/debian/tests/test_data/test5.fa (rev 0)
+++ trunk/packages/poa/trunk/debian/tests/test_data/test5.fa 2017-07-21 01:07:36 UTC (rev 23881)
@@ -0,0 +1,6 @@
+>seq1
+PKMIVRPQKNEG
+>seq2
+ALVRPQKNTRM
+>seq3
+THKMLVRNETAM
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