Natural Chromosome Layout

Features added based on feedback from reviewers at Frontiers in Genetics:

• Default Tile Layout places large chromosomes in one continuous vertical column. Tile Layout no longer has pages or rows of pages etc. as these were counter-intuitive and unbiological.
• Ideogram and Parallel layouts also updated with new defaults
• Directory and package renamed to FluentDNA
• Updating to Python 3.7 and 3.8 support #93
• New Mac release
• Parallel layout Border boxes are on by default
• --contigs argument allows you to set the order sequences will be displayed.
• pip install FluentDNA from official PyPI registry
• Visualizations output to /results/ instead of the confusing /www-data/dnadata/
• #81 Packed layout: I found that less padding is better for keeping visual patterns coherent over clusters of columns.  The white space has a disproportionate effect if you space it out too much.
• Migrated links to FluentDNA.com

Repeat Galleries

2.4.5 Changes:

• Added separate folder for Scripts
• Added: Generate an MSA directory from RepeatMasker csv. Visualize galleries of repeat content. #86
• Multiple Sequence Alignment (MSA) received many usability improvements
  • Long MSA such as SNP arrays will wrap into a rectangular image #43
  • Very Tall MSA will be capped at 1,000 rows and will wrap without disrupting the rest of the repeats
• Alignment stats showing more detail about chain membership and translocations #82
• Improved ParallelLayout bundle box decorations and enabled them by default #65
• Folders and files all renamed to FluentDNA for consistency #90

For Linux and Mac, install the latest version as a Python module with two commands (see Installation):

pip install --upgrade git+https://github.com/josiahseaman/DNASkittleUtils
pip install --upgrade git+https://github.com/josiahseaman/FluentDNA.git@pip

Publication Release

This release contains quality of life improvements:

• Server now automatically starts after a successful render #81
• Custom layouts #64
• Mouseover Sequence for MSA and Genome Alignments #62 #39 #71
• More clear visual cues for Genome Alignment columns #65
• /sources/ Downloads for reproducing any visualization #77
• Many quality of life improvements for publication #81

For Linux and Mac, install the latest version with two console commands (see Installation):

pip install --upgrade git+https://github.com/josiahseaman/DNASkittleUtils
pip install --upgrade git+https://github.com/josiahseaman/FluentDNA.git@pip

2.4.1: Ideograms and Sequence Retrieval

This release includes Windows and Mac command line binaries as well as a beta version of the GUI for Mac.
2019-03-12 : Updated Mac CommandLine version
Updated Mac GUI APP version

Pre-release GUI version for mac OS

A bundled FluentDNAgui.app for a GUI version of the application.

Download and unzip the .APP, click to run and get a GUI to launch FluentDNA operations.

FluentDNA macOS

*This release includes an updated .spec file for a MAC OS compile and the resulting distributable files built on macOS High Sierra (10.13.5).

• FluentDNA User Manual contains examples of all major tasks
• Unzippable binary for macOS, no install required.
• Download the FluentDNA.zip file, and unzip to have the following folder structure:
  FluentDNA/FluentDNA (this is the command line version of FluentDNA, run with ./FluentDNA)
  FluentDNA/DDV/
  FluentDNA/include/
  FluentDNA/lib/
  FluentDNA/[.so files and .dylib files]

FluentDNA 2.2.3 Windows

• FluentDNA User Manual contains examples of all major tasks
• Unzippable .exe for Windows, no install required.
• Explore large sets of Multiple Sequence Alignments using multi-part FASTA files for nucleotides or proteins
• Visualize a gene annotation alongside its sequence in a single step using --ref_annotation=
• Including example_data alongside the program

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.