[med-svn] [Git][med-team/lagan][master] Addeded testing for mlagan

[Lance Lin (@linqigang)]

Lance Lin pushed to branch master at Debian Med / lagan


Commits:
7383e38a by Lance Lin at 2022-03-08T20:13:26+07:00
Addeded testing for mlagan

- - - - -


3 changed files:

- debian/changelog
- debian/tests/control
- + debian/tests/run-mlagan-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+lagan (2.0-7) unstable; urgency=medium
+
+  * Team upload
+
+  [ Lance Lin ]
+  * Add autopkgtest for mlagan and order
+  * Updates d/lagan.links to add addtitional links to fix path issues
+
+ -- Lance Lin <LQi254 at protonmail.com>  Tue, 8 Mar 2022 19:48:21 +0700
+
 lagan (2.0-6) unstable; urgency=medium
 
   * Team upload


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-unit-test
+Tests: run-unit-test, run-mlagan-test
 Depends: @
 Restrictions: allow-stderr


=====================================
debian/tests/run-mlagan-test
=====================================
@@ -0,0 +1,90 @@
+#!/bin/sh
+
+# Author: Lance Lin <LQi254 at protonmail.com>
+# Date: 08 March 2022
+# File: run-mlagan-test
+# Purpose: run a unit test for the mlagan binary
+#
+# Details:
+# Use a publicly accessible .fasta file format example. There are others, but they quite large (>30MB).
+# Compare it with the included sample.fasta file in the lagan package.
+
+set -e
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+cd "${AUTOPKGTEST_TMP}"
+
+# This is needed for lagan to run
+export LAGAN_DIR=/usr/lib/lagan
+
+echo "run-mlagan-test: generating sample data"
+
+# FASTA format file from "UT Southwestern Medical Center"
+# URL: http://prodata.swmed.edu/promals/info/fasta_format_file_example.htm
+# Website title: Fasta format file example
+# Date accessed: 18 February 2022
+cat <<EOF > testfile.fasta
+>seq0
+FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
+>seq1
+KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
+>seq2
+EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
+>seq3
+MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
+>seq4
+EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
+>seq5
+SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
+>seq6
+FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
+>seq7
+SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
+>seq8
+SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
+>seq9
+KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
+>seq10
+FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK
+EOF
+
+# This is sample.fasta from the lagan package
+cat <<EOF > sample.fasta
+>sample1
+GGCATGTCCAGAAAATCCAAGTGCCTCTTCCTCTTGATCTTCTCCAACGATGTCCAGA
+AAATCCAAGTGCCTCATTCCTCTTGATCTTCTCCAGGCATGTCCAGAAAATCCAAGTG
+CCTCTTCCTCTCTGATCTTCTCCTCGGTTGGTCCAGAAAATCCAAGTGCCTCTTCCTC
+TTGATCTTCTCCAGAAATGTCCAGAAAATCCAAGTAGCCTCTTCCTCTTGATCGGCTC
+CAGAAATGTCCAGAAAAATCCAAGTGCCTCTTCCTCTTGATCGGCTCCATAAATGTCC
+AGAAAATCCAACGTGCCTCTTCCTCTTGATCGGCTCCAGAAATGTCCAGAAATATCCA
+AGTGCCTCTTCCTCTTGATCGGCTCCTTA
+>sample2
+CGATCCCAAATCCAAGTGCCTCAGAGTCTACTTGATCTTCAATTCAGATCCCAAATCC
+AAGTGCCTCAGAGTCTACTTGAATCTTCTATCGGGTCCCAAATCCAAGTGCCTCAGAG
+TCTACTTGATCTTCTCTCTCGATCCCATATCCAAGTGCCTCCTAGAGTCTACTTGATC
+TTCTCGATAACCAAAATCCAAGTGCCTCAGAGTCTACTTCACTCTTCTCGACTAACCC
+AAATCCAAGTGCCTCAGATGAGTCTACTTCCTCTTCTCATAACTCAAATCCAAGTGCC
+TCAGAGTCTAACTTCCTCTTCTCGAATAACCCAAATCCAAGTGCCTCAGAGTGTCTAC
+TTCCTCTTCTCG
+>sample3
+TACCCAAATCCAAGTGCCTCAGCGTCTAATAAAACAAGTCTTGATCTTCAACTCCTCC
+CAAATCCAAGTGCAACCTCAGCCGCTAATAAAAAGTCTTGATCTTCTCGCGTCCGGCA
+AATCCAAGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGGAGTCCCAAATCCA
+AGTGCCTCAGCGCTAATAAAAAGTCTTGATCTTCTCGGAGGAACAACAAATCCAAGTG
+CCTCAAGCGCTAATAAAAAGTCCCGATCTTCTCGTGACAATACAAATCCAAGTGCCTC
+AGCGCTAATAAAAAGTCCCGATCTTCTCCCGTGTAAACAAATCCAAGTGCCTCAGCGC
+TAATAAAAAGTCCCGATCTTCTCTGGTAACACAACAAATCCAAGTCACGCCTCAGATA
+CGCTAATAAAAAGTCCCGATCTTCTC
+EOF
+
+echo "run-mlagan-test: generating md5 sums for verification"
+echo "b7bdc0c6522f86c7c50a62ff7d27c2e9  output.txt" >> checksums
+
+echo "run-mlagan-test: running mlagan"
+mlagan sample.fasta testfile.fasta > output.txt
+
+echo "run-mlagan-test: verifying md5 checksums"
+md5sum --check checksums



View it on GitLab: https://salsa.debian.org/med-team/lagan/-/commit/7383e38a6c0d220c326193684883258906eaa439

-- 
View it on GitLab: https://salsa.debian.org/med-team/lagan/-/commit/7383e38a6c0d220c326193684883258906eaa439
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