[med-svn] [fastx-toolkit] 01/01: add autopkgtest test-suite

[Nadiya Sitdykova]

This is an automated email from the git hooks/post-receive script.

rovenskasa-guest pushed a commit to branch master
in repository fastx-toolkit.

commit 9213857d319f9390e6647260411f36715b67326f
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Mon Jun 5 18:18:31 2017 -0400

    add autopkgtest test-suite
---
 debian/README.test         |  8 +++++
 debian/changelog           |  9 ++++++
 debian/docs                |  3 ++
 debian/tests/control       |  3 ++
 debian/tests/run-unit-test | 77 ++++++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 100 insertions(+)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..973ad8a
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+________________________________________
+
+To run the unit tests provided by the package you can do 
+
+  sh run-unit-test
+
+in this directory.
diff --git a/debian/changelog b/debian/changelog
index 6825b5c..3748466 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+fastx-toolkit (0.0.14-4) unstable; urgency=low
+
+  * Team upload.
+
+  [ Nadiya Sitdykova ]
+  * Add autopkgtest test-suite
+
+ -- Nadiya Sitdykova <rovenskasa at gmail.com>  Mon, 05 Jun 2017 17:55:44 -0400
+
 fastx-toolkit (0.0.14-3) unstable; urgency=low
 
   [ Steffen Moeller ]
diff --git a/debian/docs b/debian/docs
index ffe5fe2..4e1166c 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1,3 +1,6 @@
 NEWS
 README
 THANKS
+galaxy/test-data
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..93684aa
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,77 @@
+#!/bin/sh -e
+
+pkg=fastx-toolkit
+
+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 *
+
+check () {
+  cmp -s $1 $2 || {
+    echo "incorrect result"
+    exit 1
+  }
+}
+
+echo "testing fastq_to_fasta"
+fastq_to_fasta -i fastq_to_fasta1.fastq -o out
+check fastq_to_fasta1a.out out
+fastq_to_fasta -i fastq_to_fasta1.fastq -r -n -o out
+check fastq_to_fasta1b.out out
+
+echo "testing fastx_quality_stats"
+fastx_quality_stats -i fastq_stats1.fastq -o out
+#check fastq_stats1.out out
+
+echo "testing fastx_clipper"
+fastx_clipper -i fastx_clipper1.fastq -a CAATTGGTTAATCCCCCTATATA -c -o out
+#check fastx_clipper1a.out out
+
+echo "testing fastx_renamer"
+fastx_renamer -i fastx_renamer1.fastq -n SEQ -o out
+check fastx_renamer1.out out
+
+echo "testing fastx_trimmer"
+fastx_trimmer -i fastx_trimmer1.fasta -f 5 -l 36 -o out
+check fastx_trimmer1.out out
+fastx_trimmer -i fastx_trimmer2.fastq -f 1 -l 27 -o out
+check fastx_trimmer2.out out
+
+echo "testing fastx_collapser"
+fastx_collapser -i fasta_collapser1.fasta -o out
+
+echo "testing fastx_artifacts_filter"
+fastx_artifacts_filter -i fastx_artifacts1.fasta -o out
+check fastx_artifacts1.out out
+fastx_artifacts_filter -i fastx_artifacts2.fastq -o out
+check fastx_artifacts2.out out
+
+#echo "testing fastq_quality_filter"
+#fastq_quality_filter -i fastq_qual_filter1.fastq -q 33 -p 100 -o out
+#check fastx_qual_filter1a.out out
+#fastq_quality filter -i fastq_qual_filter1.fastq -q 20 -p 100 -o out
+#check fastq_qual_filter1b.out out
+
+echo "testing fastx_reverse_complement"
+fastx_reverse_complement -i fastx_rev_comp1.fasta -o out
+check fastx_reverse_complement1.out out
+fastx_reverse_complement -i fastx_rev_comp2.fastq -o out
+check fastx_reverse_complement2.out out
+
+echo "testing fasta_formatter"
+fasta_formatter -i fasta_formatter1.fasta -o out
+check fasta_formatter1.out out
+fasta_formatter -i fasta_formatter1.fasta -w 60 -o out
+check fasta_formatter2.out out
+
+echo "testing fasta_nucleotide_changer"
+fasta_nucleotide_changer -i fasta_nuc_changer1.fasta -r -o out
+check fasta_nuc_changer1.out out
+fasta_nucleotide_changer -i fasta_nuc_changer2.fasta -d -o out
+check fasta_nuc_changer2.out out

-- 
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