diff --git a/docs/source/installation.rst b/docs/source/installation.rst index d8367ad..0b75c53 100644 --- a/docs/source/installation.rst +++ b/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. diff --git a/docs/source/releaseNotes.rst b/docs/source/releaseNotes.rst index 326167e..a42bbc3 100644 --- a/docs/source/releaseNotes.rst +++ b/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 ----------------- diff --git a/docs/source/workflows.rst b/docs/source/workflows.rst index 4b5f00a..73375e1 100644 --- a/docs/source/workflows.rst +++ b/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 .. diff --git a/utils/dnascent2bedgraph.py b/utils/dnascent2bedgraph.py index 2bcf8b0..13f88c7 100644 --- a/utils/dnascent2bedgraph.py +++ b/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)