[med-svn] [Git][med-team/sortmerna][master] 4 commits: Add autopkgtest template and README.test
Pranav Ballaney
gitlab at salsa.debian.org
Fri Mar 20 19:29:47 GMT 2020
Pranav Ballaney pushed to branch master at Debian Med / sortmerna
Commits:
2b4cc131 by Pranav Ballaney at 2020-03-19T19:01:36+05:30
Add autopkgtest template and README.test
- - - - -
fc746124 by Pranav Ballaney at 2020-03-20T02:41:41+05:30
Install examples
- - - - -
2f01fbca by Pranav Ballaney at 2020-03-21T00:57:16+05:30
Add autopkgtests
- - - - -
8202f0e5 by Pranav Ballaney at 2020-03-21T00:57:56+05:30
Update changelog
- - - - -
5 changed files:
- + debian/README.test
- debian/changelog
- + debian/examples
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+sortmerna (2.1-5) UNRELEASED; urgency=medium
+
+ * Add autopkgtest template and README.test
+ * Install examples
+ * Add autopkgtests
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Sat, 21 Mar 2020 00:57:31 +0530
+
sortmerna (2.1-4) unstable; urgency=medium
* Use 2to3 to port from Python2 to Python3
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+tests/*
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,190 @@
+#!/bin/bash
+set -e
+
+pkg=sortmerna
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+mkdir temp output
+
+echo === Test 1 ===
+echo Writing to --tmpdir
+indexdb_rna --ref data/ref_GQ099317_forward_and_rc.fasta,output/test1 --tmpdir temp
+if [ -f output/test1.kmer_0.dat ] && \
+ [ -f output/test1.bursttrie_0.dat ] && \
+ [ -f output/test1.pos_0.dat ] && \
+ [ -f output/test1.stats ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 2 ===
+echo Indexing a database using SortMeRNA
+indexdb_rna --ref data/gg_13_8_ref_set.fasta,output/test2
+if [ -f output/test2.kmer_0.dat ] && \
+ [ -f output/test2.bursttrie_0.dat ] && \
+ [ -f output/test2.pos_0.dat ] && \
+ [ -f output/test2.stats ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 3 ===
+echo Test indexing a database using SortMeRNA with m = 0.05, that is 7 parts
+indexdb_rna --ref data/gg_13_8_ref_set.fasta,output/test3 -m 0.05
+if [ -f output/test3.kmer_0.dat ] && \
+ [ -f output/test3.kmer_1.dat ] && \
+ [ -f output/test3.kmer_2.dat ] && \
+ [ -f output/test3.kmer_3.dat ] && \
+ [ -f output/test3.kmer_4.dat ] && \
+ [ -f output/test3.kmer_5.dat ] && \
+ [ -f output/test3.kmer_6.dat ] && \
+ [ -f output/test3.bursttrie_0.dat ] && \
+ [ -f output/test3.bursttrie_1.dat ] && \
+ [ -f output/test3.bursttrie_2.dat ] && \
+ [ -f output/test3.bursttrie_3.dat ] && \
+ [ -f output/test3.bursttrie_4.dat ] && \
+ [ -f output/test3.bursttrie_5.dat ] && \
+ [ -f output/test3.bursttrie_6.dat ] && \
+ [ -f output/test3.pos_0.dat ] && \
+ [ -f output/test3.pos_1.dat ] && \
+ [ -f output/test3.pos_2.dat ] && \
+ [ -f output/test3.pos_3.dat ] && \
+ [ -f output/test3.pos_4.dat ] && \
+ [ -f output/test3.pos_5.dat ] && \
+ [ -f output/test3.pos_6.dat ] && \
+ [ -f output/test3.stats ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo Generating index files for the remaining tests.
+# Tests 4, 5, 6
+indexdb_rna --ref data/silva-bac-16s-database-id85.fasta,output/bac.idx:data/silva-arc-16s-database-id95.fasta,output/arc.idx
+# Tests 7 and 8
+indexdb_rna --ref data/silva-bac-16s-database-id85.fasta,output/bac_250.idx --max_pos 250
+# Test 9
+indexdb_rna --ref data/ref_GQ099317_forward_and_rc.fasta,output/GQ099317.idx
+echo Done
+
+
+echo
+echo === Test 4 ===
+echo Test sortmerna on 3 reads against arc-16s and bac-16s databases.
+echo 2/3 reads match both arc-16s and bac-16s and 1/3 is a random read.
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac.idx:data/silva-arc-16s-database-id95.fasta,output/arc.idx \
+ --aligned output/test4aligned \
+ --reads data/set7_arc_bac_16S_database_match.fasta \
+ --log --fastx
+if [ -f output/test4aligned.fasta ] && \
+ [ -f output/test4aligned.log ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 5 ===
+echo Test sortmerna on simulated data, 10000 reads with 1% error - --aligned,
+echo 10000 reads with 10% error - de novo, 10000 reads random - --other
+echo Conditions: reference index and input query FASTA file both processed as one section.
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac.idx \
+ --aligned output/test5aligned --other output/test5other \
+ --reads data/set5_simulated_amplicon_silva_bac_16s.fasta \
+ --id 0.97 --coverage 0.97 --log --otu_map --de_novo_otu --blast "1 cigar qcov" --fastx
+if [ -f output/test5aligned.blast ] && \
+ [ -f output/test5aligned.fasta ] && \
+ [ -f output/test5aligned.log ] && \
+ [ -f output/test5aligned_denovo.fasta ] && \
+ [ -f output/test5aligned_otus.txt ] && \
+ [ -f output/test5other.fasta ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 6 ===
+echo Test sortmerna on simulated data, 10000 reads with 1% error - --aligned,
+echo 10000 reads with 10% error - de novo, 10000 reads random - --other
+echo Conditions: reference index processed as one unit and input query FASTA file in 6 sections.
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac.idx \
+ --aligned output/test6aligned --other output/test6other \
+ --reads data/set5_simulated_amplicon_silva_bac_16s.fasta \
+ --id 0.97 --coverage 0.97 --log --otu_map --de_novo_otu --blast "1 cigar qcov" --fastx -m 1
+if [ -f output/test6aligned.blast ] && \
+ [ -f output/test6aligned.fasta ] && \
+ [ -f output/test6aligned.log ] && \
+ [ -f output/test6aligned_denovo.fasta ] && \
+ [ -f output/test6aligned_otus.txt ] && \
+ [ -f output/test6other.fasta ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 7 ===
+echo Test outputting FASTA file for de novo clustering using environmental data.
+echo Conditions: input FASTA file is processed in one mapped section.
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac_250.idx \
+ --aligned output/test7aligned --id 0.97 --coverage 0.97 --log \
+ --otu_map --de_novo_otu --fastx --reads data/set2_environmental_study_550_amplicon.fasta
+if [ -f output/test7aligned.fasta ] && \
+ [ -f output/test7aligned.log ] && \
+ [ -f output/test7aligned_denovo.fasta ] && \
+ [ -f output/test7aligned_otus.txt ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 8 ===
+echo Test outputting FASTQ files for merged mate pair reads.
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac_250.idx \
+ --aligned output/test8aligned --other output/test8nonaligned \
+ --fastx --reads data/set4_mate_pairs_metatranscriptomics.fastq --log
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac_250.idx \
+ --aligned output/test8aligned --other output/test8nonaligned \
+ --paired_in --fastx --reads data/set4_mate_pairs_metatranscriptomics.fastq --log
+sortmerna --ref data/silva-bac-16s-database-id85.fasta,output/bac_250.idx \
+ --aligned output/test8aligned --other output/test8nonaligned \
+ --paired_out --fastx --reads data/set4_mate_pairs_metatranscriptomics.fastq --log
+if [ -f output/test8aligned.fastq ] && \
+ [ -f output/test8aligned.log ] && \
+ [ -f output/test8nonaligned.fastq ]; then
+ echo PASS
+else
+ echo FAIL
+fi
+
+echo
+echo === Test 9 ===
+echo Test SortMeRNAs option --num_alignments 0 which should
+echo search both forward and reverse-complement query for alignments
+sortmerna --ref data/ref_GQ099317_forward_and_rc.fasta,output/GQ099317.idx \
+ --aligned output/test9aligned --reads data/illumina_GQ099317.fasta --num_alignments 0 --sam
+if [ -f output/test9aligned.sam ]; then
+ echo PASS
+else
+ echo FAIL
+fi
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/1b6545595e5c05e78c037ab527ca4a1bf32ee34c...8202f0e5412dfa5389eadb349a006d585116d7b6
--
View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/1b6545595e5c05e78c037ab527ca4a1bf32ee34c...8202f0e5412dfa5389eadb349a006d585116d7b6
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