fix path issue with dnascent2bedgraph util

docs/source/installation.rst

@@ -16,7 +16,7 @@ The DNAscent directory will appear in your current directory. Switch to the late
 .. code-block:: console
 
    cd DNAscent
-   git checkout 2.0.0
+   git checkout 2.0.2
    make
 
 This will put the DNAscent executable into the DNAscent/bin directory. Compilation requires a version of gcc that supports C++14, and a typical compile time for DNAscent and all of its dependencies is 5-7 minutes.

docs/source/releaseNotes.rst

@@ -3,7 +3,7 @@
 Release Notes
 ===============================
 
-v2.0.0
+v2.0.2
 -----------------
 
 * Migration from HMM-based BrdU detection at every thymidine to ResNet-based detection at every thymidine,
@@ -12,7 +12,8 @@ v2.0.0
 * ``DNAscent forkSense`` to call replication origins and termination sites in both synchronously and asynchronously replicating cells at any point in S-phase,
 * ``DNAscent align`` to align nanopore signals to reference,
 * Significant increases to replication origin calling accuracy,
-* Visualisation utility for plotting output of multiple DNAscent executables as bedgraphs.
+* Visualisation utility for plotting output of multiple DNAscent executables as bedgraphs,
+* Released with `Boemo, M.A. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. bioRxiv 2020.
 
 v1.0.0
 -----------------

docs/source/workflows.rst

@@ -18,7 +18,7 @@ Download and compile DNAscent:
 
    git clone --recursive https://github.com/MBoemo/DNAscent.git
    cd DNAscent
-   git checkout 2.0.0
+   git checkout 2.0.2
    make
    cd ..
 

utils/dnascent2bedgraph.py

@@ -377,7 +377,8 @@ def parseSecondaryFile(fname, readID2directory,args):
 args = parseArguments(sys.argv[1:])
 
 #check the output 
-args.outDir = args.outDir.strip("/")
+if args.outDir[-1:] == "/":
+	args.outDir = args.outDir[:-1]
 if os.path.isdir(args.outDir):
 	print('Output directory '+args.outDir+' already exists.  Exiting.')
 	exit(0)