[med-svn] [Git][med-team/sweed][master] 2 commits: Add autopkgtests
Nilesh Patra
gitlab at salsa.debian.org
Thu Aug 27 16:29:31 BST 2020
Nilesh Patra pushed to branch master at Debian Med / sweed
Commits:
431eeb85 by Nilesh Patra at 2020-08-27T20:55:16+05:30
Add autopkgtests
- - - - -
b802aac2 by Nilesh Patra at 2020-08-27T20:55:29+05:30
Install relevant examples
- - - - -
8 changed files:
- + debian/sweed.examples
- + debian/tests/README
- + debian/tests/control
- + debian/tests/data/data.FA
- + debian/tests/data/data.VCF
- + debian/tests/data/macs.out
- + debian/tests/data/ms.out
- + debian/tests/run-unit-test
Changes:
=====================================
debian/sweed.examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for SWeeD
+=================
+
+The data for tests has been referenced from:
+ https://cme.h-its.org/exelixis/resource/download/software/sweed3.0_manual.pdf
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+
=====================================
debian/tests/data/data.FA
=====================================
@@ -0,0 +1,17 @@
+>D_sec
+GTTGTTTAAATACCAATCGATTTGCATTCAAGTTTGAGAATTCTAGGATTTTTCAATTTT
+>Dmel_A82_1230
+GTTGTTTAAA-------------GCATTTAAT-GTTTCAGCCATACGACTCTTCA-----
+>Dmel_A84_1230
+GTTGATTAGA-------------GCATTTAAT-CTTTCAGCCATACGACTCTTCA-----
+>Dmel_A95_1230
+GTTGTTTAAA-------------GCATTTAAT-CTTTCAGCCATACGACTCTTCA-----
+//
+>D_seq1
+GTTGTTTAAATACCAATCGATTTGCATTCAAGTTTGAGAATTCTAGGATTTTTCAATTTT
+>D2
+GTTGTTTAAA-------------GCATTTAAT-GTTTCAGCCATACGACTCTTCA-----
+>D3
+GTTGATTAGA-------------GCATTTAAT-CTTTCAGCCATACGACTCTTCA-----
+>D4
+GTTGTTTAAA-------------GCATTTAAT-CTTTCAGCCATACGACTCTTCA-----
\ No newline at end of file
=====================================
debian/tests/data/data.VCF
=====================================
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
+20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
+20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
+20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
\ No newline at end of file
=====================================
debian/tests/data/macs.out
=====================================
@@ -0,0 +1,24 @@
+COMMAND: macs 40 22422 -t 0.0001 -r 0.043 -h 5e4 -eN 0.036744 0.00204
+-eN 0.0375 8.0 -eN 0.1395 1.5 -s 417790 -i 2
+SEED: 417790
+SITE: 0 1.197754e-1 1000000000000000000000000000000000000000
+SITE: 1 0.232366639 0000000000000000100000000000000000000000
+SITE: 2 0.244833485 0110110100011101011110000101110100010001
+SITE: 3 0.30002599 0000000000000000000010000000000000000000
+SITE: 4 0.878531842 1110000000100001000010000010011001100011
+SITE: 5 0.914214234 1000010000100001000110001110010001110111
+TOTAL_SAMPLES: 40
+TOTAL_SITES: 6
+BEGIN_SELECTED_SITES
+0 1 2 3 4 5
+END_SELECTED_SITES
+SITE: 0 0.117200364 1100110000001010000001001001000000000000
+SITE: 1 0.295165608 1000100000100001000011000001010000010001
+SITE: 2 0.424410309 1110111100111111101111011010111011011011
+SITE: 3 0.562284003 0000001000000100100000000000000000000000
+SITE: 4 0.704560616 0000000010000000000000000000000000000000
+TOTAL_SAMPLES: 40
+TOTAL_SITES: 5
+BEGIN_SELECTED_SITES
+0 1 2 3 4
+END_SELECTED_SITES
\ No newline at end of file
=====================================
debian/tests/data/ms.out
=====================================
@@ -0,0 +1,21 @@
+ms 5 2 -t 3
+53303 53650 13864
+
+//
+segsites: 6
+positions: 0.4478 0.5128 0.5537 0.6123 0.7253 0.7368
+ 000100
+%% 101010
+010001
+101000
+101010
+
+//
+segsites: 4
+positions: 0.0747 0.1319 0.4368 0.5681
+0000
+1100
+0000
+0010
+0011
+
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,30 @@
+#!/bin/bash
+set -e
+
+pkg=sweed
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+echo 'Test 1'
+SweeD -name test1 -input ms.out -grid 15 -length 1000
+echo "PASS"
+
+echo 'Test 2'
+SweeD -name test3 -input macs.out -length 10000 -grid 100
+echo "PASS"
+
+echo 'Test 3'
+SweeD -name test -input data.VCF -grid 15
+echo "PASS"
+
+echo 'Test 4'
+SweeD -name test -input data.FA -grid 15
+echo "PASS"
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/888e0f889d90ef20c45fccd0b9722382499434e9...b802aac288a2460b2e0481308bdd0313927353a5
--
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/888e0f889d90ef20c45fccd0b9722382499434e9...b802aac288a2460b2e0481308bdd0313927353a5
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