[med-svn] [Git][med-team/mecat2][master] Add test data and write some autopkgtest

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / mecat2


Commits:
97769cd4 by Shayan Doust at 2020-07-02T21:05:37+01:00
Add test data and write some autopkgtest

- - - - -


4 changed files:

- + debian/source/include-binaries
- + debian/tests/ecoli_config_file.txt
- + debian/tests/ecoli_filtered.fastq.gz
- debian/tests/run-unit-test


Changes:

=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,2 @@
+debian/tests/ecoli_filtered.fastq.gz
+debian/tests/ecoli_config_file.txt


=====================================
debian/tests/ecoli_config_file.txt
=====================================
@@ -0,0 +1,17 @@
+PROJECT=ecoli
+RAWREADS=ecoli_filtered.fastq
+GENOME_SIZE=4800000
+THREADS=4
+MIN_READ_LENGTH=2000
+CNS_OVLP_OPTIONS="-kmer_size 13"
+CNS_PCAN_OPTIONS="-p 100000 -k 100"
+CNS_OPTIONS=""
+CNS_OUTPUT_COVERAGE=30
+TRIM_OVLP_OPTIONS="-skip_overhang"
+TRIM_PM4_OPTIONS="-p 100000 -k 100"
+TRIM_LCR_OPTIONS=""
+TRIM_SR_OPTIONS=""
+ASM_OVLP_OPTIONS=""
+FSA_OL_FILTER_OPTIONS="--max_overhang=-1 --min_identity=-1"
+FSA_ASSEMBLE_OPTIONS=""
+CLEANUP=0


=====================================
debian/tests/ecoli_filtered.fastq.gz
=====================================
Binary files /dev/null and b/debian/tests/ecoli_filtered.fastq.gz differ


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,8 +1,6 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
-
 export LC_ALL=C.UTF-8
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -12,8 +10,16 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a debian/tests/ecoli_filtered.fastq.gz debian/tests/ecoli_config_file.txt \
+	"${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
+# Extract the test data
+gunzip ecoli_filtered.fastq.gz
+
+# Trim out low quality subsequences in corrected reads
+mecat trim ecoli_config_file.txt
+
+# Assemble contigs using the trimmed reads
+mecat assemble ecoli_config_file.txt



View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8

-- 
View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8
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