Merge pull request #223 from smithlabcode/test-xcounts-unxcounts

Adding tests for xcounts and unxcounts

Makefile.am

@@ -99,6 +99,8 @@ EXTRA_DIST = \
              test_scripts/test_amrfinder.test \
              test_scripts/test_hypermr.test \
              test_scripts/test_diff.test \
+             test_scripts/test_xcounts.test \
+             test_scripts/test_unxcounts.test \
              test_scripts/test_mlml.test
 
 ### ADS: Testing with `make check` can be a long process. Testing with
@@ -126,6 +128,8 @@ TESTS = test_scripts/test_abismalidx.test \
         test_scripts/test_amrfinder.test \
         test_scripts/test_hypermr.test \
         test_scripts/test_diff.test \
+        test_scripts/test_xcounts.test \
+        test_scripts/test_unxcounts.test \
         test_scripts/test_mlml.test
 
 TEST_EXTENSIONS = .test
@@ -141,6 +145,8 @@ test_scripts/test_selectsites.log: test_scripts/test_counts.log
 test_scripts/test_sym.log: test_scripts/test_counts.log
 test_scripts/test_hmr.log: test_scripts/test_sym.log
 test_scripts/test_roi.log: test_scripts/test_sym.log
+test_scripts/test_xcounts.log: test_scripts/test_counts.log
+test_scripts/test_unxcounts.log: test_scripts/test_xcounts.log
 
 noinst_LIBRARIES = libdnmtools.a
 libdnmtools_a_SOURCES = \
@@ -262,4 +268,6 @@ CLEANFILES = \
     tests/araTha1_simulated.hypermr \
     tests/methylome_ab.diff \
     tests/methylome.pmd \
+    tests/reads.xcounts \
+    tests/reads.unxcounts \
     tests/mlml.out

data/md5sum.txt

@@ -20,3 +20,5 @@ d41d8cd98f00b204e9800998ecf8427e  tests/two_epialleles.amr
 6bbf66748e2a11d5c2736a81efeac270  tests/reads.fmt.sam
 f963e689859dcf38a26acda9a65a6431  tests/reads.sam
 a751b849e0895b2403f8ddd01b647ae1  tests/reads.fmt.srt.uniq.sam
+abb472bdea230af31e0d2b00abb95b02  tests/reads.xcounts
+12e0afdca1387b2805cfee0ea2ddcfea  tests/reads.unxcounts

test_scripts/test_unxcounts.test

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+infile1=tests/reads.xcounts
+infile2=tests/tRex1.fa
+outfile=tests/reads.unxcounts
+if [[ -e "${infile1}" && -e "${infile2}" ]]; then
+    ./dnmtools unxcounts -c ${infile2} -o ${outfile} ${infile1}
+    x=$(md5sum -c tests/md5sum.txt | grep "${outfile}:" | cut -d ' ' -f 2)
+    if [[ "${x}" != "OK" ]]; then
+        exit 1;
+    fi
+else
+    echo "unxcounts input file not found; skipping remaining tests";
+    exit 77;
+fi

test_scripts/test_xcounts.test

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+infile1=tests/reads.counts
+infile2=tests/tRex1.fa
+outfile=tests/reads.xcounts
+if [[ -e "${infile1}" && -e "${infile2}" ]]; then
+    ./dnmtools xcounts -c ${infile2} -o ${outfile} ${infile1}
+    x=$(md5sum -c tests/md5sum.txt | grep "${outfile}:" | cut -d ' ' -f 2)
+    if [[ "${x}" != "OK" ]]; then
+        exit 1;
+    fi
+else
+    echo "xcounts input file(s) not found; skipping test";
+    exit 77;
+fi