drawtetrado 1.2

Draw simplified, layer diagrams of quadruplexes.

Project description

DrawTetrado is a Python application to visualize quadruplexes and G4-helices in DNA and RNA structures. It generates publication-quality SVG files containing layer diagrams. They show the tetrads as a stack, with each position having four nucleobases colored according to anti or syn conformation. In addition, DrawTetrado visualizes the strands with arrows for an accessible overview of their directionality and visual determination of loop types.

DrawTetrado automatically optimizes the layout. The result is a visually pleasing and readable image, even for the most complex cases like V-loops and G4-helices (dimers).

Installation

pip install drawtetrado

Dependencies

The project is written in Python 3.6+ and requires pycairo and svgwrite. The internal optimization routine is written in C++ and requires Cython and a C++20-compliant compiler (e.g. GCC 8+).

DrawTetrado parses the output of ElTetrado (Zok et al., 2022; Popenda et al., 2020; Zok et al., 2020). If you do not have that installed, please install DSSR (Lu et al., 2015) and run:

pip install eltetrado

Usage

usage: drawtetrado [-h] [--angle ANGLE] [--tetrad-spacing TETRAD_SPACING]
                   [--nucl-longer NUCL_LONGER] [--nucl-shorter NUCL_SHORTER]
                   [--nucl-spacing NUCL_SPACING] [--line-width LINE_WIDTH]
                   [--no-label-tilted] [--no-label-nucleotide-full]
                   [--no-label-nucleotide] [--no-label-chain] [--no-label-number]
                   [--label-font LABEL_FONT] [--label-size LABEL_SIZE]
                   [--se-label-size SE_LABEL_SIZE]
                   [--se-label-spacing SE_LABEL_SPACING]
                   [--color-connection COLOR_CONNECTION]
                   [--color-border COLOR_BORDER] [--color-text COLOR_TEXT]
                   [--color-gb-anti COLOR_GB_ANTI] [--color-gb-syn COLOR_GB_SYN]
                   [--color-gb-unknown COLOR_GB_UNKNOWN]
                   input output

positional arguments:
  input                 path to input JSON generated by ElTetrado
  output                path to output SVG file template

optional arguments:
  -h, --help            show this help message and exit
  --angle ANGLE         Angle of the resulted drawing in degrees. Angle between
                        front and left edges of the drawing. Reasonable values are
                        probably within 70 and 40 deg. [default=50.0]
  --tetrad-spacing TETRAD_SPACING
                        Spacing between tetrad layers. Spacing of 0 will result in
                        back edge of lower layer aligning with front edge of the
                        higher layer. [default=50.0]
  --nucl-longer NUCL_LONGER
                        Length of the "longer" edge of the nucleotide box. This
                        value should be larger than --nucl-shorter to preserve
                        proper visualization of ONZ positive and negative
                        classification of the tetrad. [default=100.0]
  --nucl-shorter NUCL_SHORTER
                        Lenght of the "shorter" edge of the nucleotide box. This
                        value should be smaller than --nucl-longer to preserve
                        proper visualization of ONZ positive and negative
                        classification of the tetrad. [default=70.0]
  --nucl-spacing NUCL_SPACING
                        Spacing between individual nucleotides in the same tetrad
                        layer. [default=10.0]
  --line-width LINE_WIDTH
                        Width of the lines on the drawing. Exact witdth of
                        connection lines, tetrad border line. Points at the corners
                        of tetrads are using 70% of this value as width.
                        [default=3.0]
  --no-label-tilted     By default labels are skewed and put on labels. This means
                        the text skew is affected by the --angle of the drawing and
                        can be less readable with some configurations. Disabling it
                        will at most rotate the text instead of skewing it.
  --no-label-nucleotide-full
                        Exclude full name from the nucleotide label. Includes naming
                        like DG instead of G, BRU instead of u. Full labels can
                        provide more information about nucleotides.
  --no-label-nucleotide
                        Exclude name from the nucleotide label like A, C, T, G
                        Setting this flag also sets --no-label-nucleotide-full.
  --no-label-chain      Exclude chain information from the nucleotide label.
  --no-label-number     Exclude nucleotide index from the nucleotide label.
  --label-font LABEL_FONT
                        Font family used for all labels.
                        [default="Arial, Helvetica"]
  --label-size LABEL_SIZE
                        Font size of the nucleotide labels only. [default=20.0]
  --se-label-size SE_LABEL_SIZE
                        Font size of 5' and 3' labels only. [default=24.0]
  --se-label-spacing SE_LABEL_SPACING
                        Spacing between 5', 3' labels and nucleotide. Can put
                        further away or closer to prevent potential overlap with
                        strand between nucleotides. [default=20.0]
  --color-connection COLOR_CONNECTION
                        Color of connecting line between nucleotides in hex.
                        [default="#000000"]
  --color-border COLOR_BORDER
                        Color of rectangular border of tetrad layer in hex.
                        [default="#E23D28"]
  --color-text COLOR_TEXT
                        Color of nucleotide labels and 5' 3' labels in hex.
                        [default="#000000"]
  --color-gb-anti COLOR_GB_ANTI
                        Color of nucleotide box with anti glycosidic bond in hex.
                        [default="#FFCC38"]
  --color-gb-syn COLOR_GB_SYN
                        Color of nucleotide box with anti glycosidic bond in hex.
                        [default="#FF992B"]
  --color-gb-unknown COLOR_GB_UNKNOWN
                        Color of nucleotide box with unknown glycosidic bond in hex.
                        [default="#BB9977"]


The output path is a template. For example, if output=/tmp/out.svg, the
resulting files will be /tmp/out_0.svg, /tmp/out_1.svg and so on (for as many
distinct quadruplexes as there are in the input file)

Visual customization

DrawTetrado allows for wide veriaty of changes to the visual representation of the resulting drawing. The presented drawing should provide a visual aid with which arguments impact which exect aspects of the drawing.

Nucleotide labels are made from 3 parts:

  A.DG12
  A  - Chain of the nucleotide. If --no-label-chain is set, this information (and .)
       is not included in the creation of the labels.
  DG - Full name of the nucleotide. Setting --no-label-nucleotide-full will result
       in normal short names like A, C, T, G. --no-label-nucleotide will remove
       nucleotide name part altogether.
  12 - Index of the nucleotide. Can be removed with --no-label-number

Examples of how A.DG12 label would look like with different label options:

A.DG12 - Default
A.G12  - --no-label-nucleotide-full
A.12   - --no-label-nucleotide
DG12   - --no-label-chain
A.DG   - --no-label-number
A      - --no-label-number --no-label-nucleotide

Examples

Human telomere DNA quadruplex

V-loop

G4-helix (dimer)

Bibliography

1. ONQUADRO: a database of experimentally determined quadruplex structures. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk. Nucleic Acids Research. 2022. 50(D1):D253–D258. doi:10.1093/nar/gkab1118

2. Topology-based classification of tetrads and quadruplex structures. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk. Bioinformatics. 2020. 36(4):1129–1134. doi:10.1093/bioinformatics/btz738

3. ElTetrado: a tool for identification and classification of tetrads and quadruplexes. T. Zok, M. Popenda, M. Szachniuk. BMC Bioinformatics. 2020. 21(1):40. doi:10.1186/s12859-020-3385-1

4. DSSR: an integrated software tool for dissecting the spatial structure of RNA. X.-J. Lu, H.J. Bussemaker, W.K. Olson. Nucleic Acids Research. 2015. 43(21):e142. doi:f73r8c