Merge pull request #8 from cokelaer/main

add more tools

test/test_parser.py

@@ -4,11 +4,21 @@
 import sys
 
 # for testing we do not want to install all those tools/software so
-# we have set testing=True, in which case some sanity checks and 
+# we have set testing=True, in which case some sanity checks and
 # error won't be raised.
-#def get_version(standalone):
+# def get_version(standalone):
 #    return get_version_orig(standalone, testing=True)
 
+#The mocker which is set so that when we test the presence of e.G. macs3, which is not installed,
+#no error is raise
+
+
+def test_macs3(fp, mocker):
+    mocker.patch('shutil.which', return_value="something")
+    fp.register(["macs3", "--version"], stdout=["macs3 3.0.0b1"])
+    assert get_version("macs3") == "3.0.0b1"
+
+
 def test_kallisto(fp, mocker):
     mocker.patch('shutil.which', return_value="something")
     fp.register(["kallisto", "version"], stdout=["kallisto, version 0.48.0"])
@@ -33,32 +43,33 @@ def _test_bwa(fp, mocker):
 
 
 def test_bedtools(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["bedtools", "--version"], stdout=["bedtools v2.30.0"])
     assert get_version("bedtools") == "2.30.0"
 
 
 def test_bamtools(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["bamtools", "--version"], stdout=["bamtools 2.5.2"])
     assert get_version("bamtools") == "2.5.2"
 
 
 def test_singularity(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["singularity", "version"], stdout=["3.6.2+12-gad3457a9a"])
     assert get_version("singularity") == "3.6.2+12-gad3457a9a"
 
 
 def test_script(fp, mocker):
     from click.testing import CliRunner
+
     runner = CliRunner()
 
     fp.register(["bedtools", "--version"], stdout=["bedtools v2.30.0"])
-    mocker.patch('shutil.which', return_value="bedtools")
+    mocker.patch("shutil.which", return_value="bedtools")
 
     result = runner.invoke(main, ["bedtools"])
-    print(result )
+    print(result)
 
 
 def test_bedtools_error():
@@ -69,6 +80,7 @@ def test_bedtools_error():
     except SystemExit:
         assert True
 
+
 def test_no_standalone():
     try:
         get_version("unknown_tool")

versionix/registry.py

@@ -16,7 +16,7 @@
     "bedtools": {"options": "--version", "parser": lambda x: x.stdout.split()[1][1:]},
     "bowtie": {"options": "--version", "parser": lambda x: x.stdout.split()[2]},
     "bowtie2": {"options": "--version", "parser": lambda x: x.stdout.split()[2]},
-    "bwa": {"parser": lambda x: x.stderr.strip().split("\n")[1].split()[1], "citation": "undefined"},
+    "bwa": {"parser": lambda x: x.stderr.strip().split("\n")[1].split()[1]},
     "cutadapt": {"options": "--version"},
     "deeptools": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
     "DESeq2": {
@@ -28,9 +28,16 @@
     "featureCounts": {"parser": lambda x: x.stderr.split("\n")[1].split()[1], "citation": "undefined"},
     "freebayes": {"options": "--version", "parser": lambda x: x.stdout.split()[1][1:]},
     "gffread": {"options": "--version"},
+    "jellyfish": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
     "kallisto": {"options": "version", "parser": lambda x: x.stdout.split()[2]},
+    "macs3": {
+        "options": "--version",
+        "parser": lambda x: x.stdout.split()[1],
+    },
     "minimap2": {"options": "--version"},
     "multiqc": {"options": "--version", "parser": lambda x: x.stdout.split()[2]},
+    "plotCorrelation": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
+    "plotFingerprint": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
     "salmon": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
     "samtools": {"options": "--version", "parser": lambda x: x.stdout.split()[1]},
     "seqtk": {"parser": lambda x: x.stderr.split("\n")[2].split()[1], "citation": "undefined"},