Merge pull request #396 from lldelisle/mkdir

Mkdir

Author: joachimwolff

docs/content/releases/3.7.rst

@@ -41,6 +41,8 @@ Minor enhancements:
 
 - the help message for BED has been improved to highlight the fact that the extension needs to be part of the output.
 
+- if the directory of the output file does not exists, it is created.
+
 Drop support for python 3.6
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

pygenometracks/plotTracks.py

@@ -142,6 +142,7 @@
 """
 
 import sys
+import os
 import argparse
 import warnings
 
@@ -275,6 +276,10 @@ def main(args=None):
                      track_label_width=args.trackLabelFraction,
                      plot_regions=regions, plot_width=args.plotWidth)
 
+    # Create dir if dir does not exists:
+    # Modified from https://stackoverflow.com/questions/12517451/automatically-creating-directories-with-file-output
+    os.makedirs(os.path.dirname(os.path.abspath(args.outFileName)), exist_ok=True)
+
     # Plot them
     if args.BED:
         name = args.outFileName.split(".")

pygenometracks/tests/test_tracks_label.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 import matplotlib as mpl
 from matplotlib.testing.compare import compare_images
-from tempfile import NamedTemporaryFile
+from tempfile import NamedTemporaryFile, TemporaryDirectory
 import os.path
 import pygenometracks.plotTracks
 mpl.use('agg')
@@ -148,3 +148,21 @@ def test_fixed_height():
     assert res is None, res
 
     os.remove(outfile.name)
+
+
+def test_non_existing_dir():
+
+    outdir = TemporaryDirectory()
+    output_file = os.path.join(outdir.name, "pGT_test", "test.png")
+    ini_file = os.path.join(ROOT, "title.ini")
+    region = "X:3000000-3500000"
+    expected_file = os.path.join(ROOT, 'master_title_0.2.png')
+    args = f"--tracks {ini_file} --region {region} "\
+           "--trackLabelFraction 0.2 --width 38 --dpi 130 "\
+           f"--outFileName {output_file}".split()
+    pygenometracks.plotTracks.main(args)
+    res = compare_images(expected_file,
+                         output_file, tolerance)
+    assert res is None, res
+
+    outdir.cleanup()