Lance Lin pushed to branch master at Debian Med / lagan
Commits: ad13e6c2 by Lance Lin at 2022-02-18T21:24:18+07:00 Added autopkgtest - - - - - 2 changed files: - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,90 @@ +#!/bin/sh + +# Author: Lance Lin <[email protected]> +# Date: 18 February 2022 +# File: run-unit-test +# Purpose: run a simple-unit test for the lagan package +# +# 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-unit-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-unit-test: generating md5 sums for verification" +echo "bb24ed1e1fb416d76a27580cd874c1f7 output.txt" >> checksums + +echo "run-unit-test: running lagan/order" +order testfile.fasta sample.fasta > output.txt + +echo "run-unit-test: verifying md5 checksums" +md5sum --check checksums View it on GitLab: https://salsa.debian.org/med-team/lagan/-/commit/ad13e6c22bd86a538bd6e4a0ee2120220a76091b -- View it on GitLab: https://salsa.debian.org/med-team/lagan/-/commit/ad13e6c22bd86a538bd6e4a0ee2120220a76091b You're receiving this email because of your account on salsa.debian.org.
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