update test

Author: cokelaer

test/test_main.py

@@ -0,0 +1,49 @@
+import easydev
+import os
+import tempfile
+import subprocess
+import sys
+from sequana.pipelines_common import get_pipeline_location as getpath
+
+sharedir = getpath('bioconvert')
+
+
+def test_standalone_subprocess():
+    directory = tempfile.TemporaryDirectory()
+    cmd = """sequana_pipelines_bioconvert --input-directory {}
+            --input-pattern "*fastq.gz" --input-ext fastq.gz --output-ext fasta.gz
+            --working-directory {} --force --command fastq2fasta
+          """.format(sharedir, directory.name)
+    subprocess.call(cmd.split())
+
+
+def test_standalone_script():
+    directory = tempfile.TemporaryDirectory()
+    import sequana_pipelines.bioconvert.main as m
+    sys.argv = ["test", "--input-directory", sharedir,
+            "--working-directory", directory.name, "--force",
+            "--input-pattern", '"*fastq.gz"', "--input-ext", "fastq.gz",
+            "--output-ext", "fasta.gz",
+            "--command", "fastq2fasta"]
+    m.main()
+
+def test_full():
+
+    with tempfile.TemporaryDirectory() as directory:
+        print(directory)
+        wk = directory
+
+        cmd = "sequana_pipelines_bioconvert --input-directory {} "
+        cmd += "--working-directory {}  --force --command fastq2fasta"
+        cmd += '--input-pattern "*fastq.gz" --input-ext fastq.gz'
+        cmd += "--output-ext fasta.gz "
+        cmd = cmd.format(sharedir, wk)
+        subprocess.call(cmd.split())
+
+        stat = subprocess.call("sh bioconvert.sh".split(), cwd=wk)
+
+
+def test_version():
+    cmd = "sequana_pipelines_bioconvert --version"
+    subprocess.call(cmd.split())
+