Bugfix/billgreenwald/formatbedpe miscall (#20)

* missed an argument in formatbedpe; realized coverage of tests didn't check the actual command line tool so added tests for those to prevent this issue in the future

* bumped version and pushed poetry

* black

* black

.gitignore

@@ -4,4 +4,4 @@
 */.ipynb*
 */*/.ipynb*
 __pycache__*
-poetry.lock
+.idea/workspace.xml

Module/PyGLtools/column_flip.py

@@ -127,4 +127,4 @@ def formatbedpe(A, header):
 
     header, A = _processFile(args["a"], args["stdInA"])
 
-    formatbedpe(A)
+    formatbedpe(A, header)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "PyGLtools"
-version = "3.0.0"
+version = "3.0.1"
 description = "A genomic arithmetic tool for HiC or other paired-locus data"
 authors = ["Bill Young Greenwald <billyounggreenwald@gmail.com>"]
 license = "BSD3"

tests/test_command_line_interface.py

@@ -0,0 +1,121 @@
+import subprocess
+from pathlib import Path
+from parametrization import Parametrization
+
+ASSET_DIR = Path(__file__).parent
+PYTHON_FILE_DIR = ASSET_DIR / "../Module/PyGLtools/"
+
+##can parameterize this in a sec
+
+
+@Parametrization.autodetect_parameters()
+@Parametrization.case(
+    name="browser",
+    script=PYTHON_FILE_DIR / "browser.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="closest",
+    script=PYTHON_FILE_DIR / "closest.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.sorted.pgl",
+)
+@Parametrization.case(
+    name="closest1D",
+    script=PYTHON_FILE_DIR / "closest1D.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.bed",
+)
+@Parametrization.case(
+    name="formatbedpe",
+    script=PYTHON_FILE_DIR / "column_flip.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="condense",
+    script=PYTHON_FILE_DIR / "condense.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="conveRt",
+    script=PYTHON_FILE_DIR / "conveRt.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="coverage",
+    script=PYTHON_FILE_DIR / "coverage.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.sorted.pgl",
+)
+@Parametrization.case(
+    name="expand",
+    script=PYTHON_FILE_DIR / "expand.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="findLoops",
+    script=PYTHON_FILE_DIR / "findLoops.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="intersect",
+    script=PYTHON_FILE_DIR / "intersect.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.sorted.pgl",
+)
+@Parametrization.case(
+    name="intersect1D",
+    script=PYTHON_FILE_DIR / "intersect1D.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.bed",
+)
+@Parametrization.case(
+    name="juicebox",
+    script=PYTHON_FILE_DIR / "juicebox.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="merge",
+    script=PYTHON_FILE_DIR / "merge.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="samTopgl",
+    script=PYTHON_FILE_DIR / "samTopgl.py",
+    input_file_1=ASSET_DIR / "fixtures/test_sam.sam",
+    input_file_2="",
+)
+@Parametrization.case(
+    name="subtract",
+    script=PYTHON_FILE_DIR / "subtract.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.sorted.pgl",
+)
+@Parametrization.case(
+    name="subtract1D",
+    script=PYTHON_FILE_DIR / "subtract1D.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2=ASSET_DIR / "fixtures/file.B.bed",
+)
+@Parametrization.case(
+    name="window",
+    script=PYTHON_FILE_DIR / "window.py",
+    input_file_1=ASSET_DIR / "fixtures/file.A.sorted.pgl",
+    input_file_2="",
+)
+def test_command_line(script, input_file_1, input_file_2):
+
+    if input_file_2 == "":
+        res = subprocess.run(["python", script, "-a", input_file_1])
+    else:
+        res = subprocess.run(["python", script, "-a", input_file_1, "-b", input_file_2])
+
+    res.check_returncode()