* [FluentDNA User Manual](https://github.com/josiahseaman/FluentDNA/wiki) contains examples of all major tasks
* Unzippable .exe for Windows, no install required.
* Explore large sets of [Multiple Sequence Alignments](https://github.com/josiahseaman/FluentDNA/wikimultiple-sequence-alignment-families) using multi-part FASTA files for nucleotides or proteins
* Visualize a [gene annotation](https://github.com/josiahseaman/FluentDNA/wikiannotated-genomes) alongside its sequence in a single step using `--ref_annotation=`
* Including example_data alongside the program
DDV_2.0_Pre
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.