DDV 2.0: Windows Pre-Release

To install DDV binaries, simply unzip DDV.zip and use DDV/DDV.exe in its current folder. DDV will not be added to your PATH automatically, so you'll need to navigate to the directory in command prompt. For convenience, I recommend leaving a shortcut to DDV.exe on your desktop. You can drag a FASTA file directly onto the program icon and it will convert the fasta to a png in the same directory. This is a quick way to check the contents of a file without creating an entire webpage and zoom stack.

For opening large PNG files (>100MB) in Windows, I recommend 'Windows Photo Viewer', which is not the default file association in Windows 10.

usage: DDV.exe [-h] [--quick] [-f FASTA] [-o OUTPUT_NAME] [-r] [-s]
               [-l {original,tiled,parallel,unique,transposon}]
               [-x EXTRA_FASTAS [EXTRA_FASTAS ...]] [-nt] [-nw] [-q]
               [-c CHAIN_FILE] [-ch CHROMOSOMES [CHROMOSOMES ...]] [-t] [-g]
               [-k] [-a] [-ra REF_ANNOTATION] [-qa QUERY_ANNOTATION]
               [-i IMAGE] [-n] [-v]

optional arguments:
  -h, --help            show this help message and exit
  --quick               Shortcut for dropping the file on DDV.exe. Only an
                        image will be generated in the same directory as the
                        FASTA. This is the default behavior if you drop a file
                        onto the program or a filepath is the only argument.
  -f FASTA, --fasta FASTA
                        Path to main FASTA file to process into new
                        visualization.
  -o OUTPUT_NAME, --outname OUTPUT_NAME
                        What to name the output folder (not a path). Defaults
                        to name of the fasta file.
  -r, --runserver       Run Web Server after computing.
  -s, --sort_contigs    Sort the entries of the fasta file by length. This
                        option will kick in automatically if your file has
                        more than 10,000 separate FASTA entries.
  -l {original,tiled,parallel,unique,transposon}, --layout {original,tiled,parallel,unique,transposon}
                        The type of layout to perform. Will autodetect between
                        Tiled and Parallel. Really only need if you want the
                        Original DDV layout or Unique only layout.
  -x EXTRA_FASTAS [EXTRA_FASTAS ...], --extrafastas EXTRA_FASTAS [EXTRA_FASTAS ...]
                        Path to secondary FASTA files to process when doing
                        Parallel layout.
  -nt, --no_titles      No gaps for a title. Useful when combined with
                        separate_translocations
  -nw, --no_webpage     Use if you only want an image. No webpage or zoomstack
                        will be calculated. You can use --image option later
                        to resume the process to get a deepzoom stack.
  -q, --trial_run       Only show the first 1 Mbp. This is a fast run for
                        testing.
  -c CHAIN_FILE, --chainfile CHAIN_FILE
                        Path to Chain File when doing Parallel Comparisons
                        layout.
  -ch CHROMOSOMES [CHROMOSOMES ...], --chromosomes CHROMOSOMES [CHROMOSOMES ...]
                        Chromosome to parse from Chain File. NOTE: Defaults to
                        'chr21' for testing.
  -t, --separate_translocations
                        Don't edit in translocations, list them at the end.
  -g, --squish_gaps     If two gaps are approximately the same size, subtract
                        the intersection.
  -k, --show_translocations_only
                        Used to highlight the locations of translocations
                        (temporary)
  -a, --aligned_only    Don't show the unaligned pieces of ref or query
                        sequences.
  -ra REF_ANNOTATION, --ref_annotation REF_ANNOTATION
                        Path to Annotation File for Reference Genome (first).
  -qa QUERY_ANNOTATION, --query_annotation QUERY_ANNOTATION
                        Path to Annotation File for Query Genome (second).
  -i IMAGE, --image IMAGE
                        Path to already computed big image to process with
                        DeepZoom. No layout will be performed if an image is
                        passed in.
  -n, --update_name     Query for the name of this program as known to the
                        update server
  -v, --version         Get current version of program.