pgv-mmseqs CLI Document

pgv-mmseqs is one of the CLI workflows in pyGenomeViz for visualization of homologous CDSs using MMseqs. It can be used to visualize reciprocal best-hit CDSs between each genome.

Installation

Additional installation of MMseqs is required.

Conda

conda install -c conda-forge -c bioconda pygenomeviz mmseqs2

Pip

pip install pygenomeviz

After pip installation, download MMseqs binary from release page and add PATH.

Usage

Basic Command

pgv-mmseqs --gbk_resources seq1.gbk seq2.gbk seq3.gbk seq4.gbk -o mmseqs_example

Options

General Options:
  --gbk_resources IN [IN ...]  Input genome genbank file resources
                               User can optionally specify genome range and reverse complement.
                               - Example1. Set 100 - 1000 range 'file:100-1000'
                               - Example2. Set reverse complement 'file::-1'
                               - Example3. Set 100 - 1000 range of reverse complement 'file:100-1000:-1'
  -o OUT, --outdir OUT         Output directory
  --format  [ ...]             Output image format ('png'[*]|'jpg'|'svg'|'pdf'|`html`[*])
  --reuse                      Reuse previous result if available
  -v, --version                Print version information
  -h, --help                   Show this help message and exit

MMseqs Options:
  -e , --evalue                MMseqs RBH search E-value parameter (Default: 1e-03)
  --min_identity               Min-identity threshold to be plotted (Default: 0)
  -t , --thread_num            Threads number parameter (Default: MaxThread - 1)

Figure Appearence Options:
  --fig_width                  Figure width (Default: 15)
  --fig_track_height           Figure track height (Default: 1.0)
  --feature_track_ratio        Feature track ratio (Default: 1.0)
  --link_track_ratio           Link track ratio (Default: 5.0)
  --tick_track_ratio           Tick track ratio (Default: 1.0)
  --track_labelsize            Track label size (Default: 20)
  --tick_labelsize             Tick label size (Default: 15)
  --normal_link_color          Normal link color (Default: 'grey')
  --inverted_link_color        Inverted link color (Default: 'red')
  --align_type                 Figure tracks align type ('left'|'center'[*]|'right')
  --tick_style                 Tick style ('bar'|'axis'|None[*])
  --feature_plotstyle          Feature plot style ('bigarrow'[*]|'arrow')
  --arrow_shaft_ratio          Feature arrow shaft ratio (Default: 0.5)
  --feature_color              Feature color (Default: 'orange')
  --feature_linewidth          Feature edge line width (Default: 0.0)
  --colorbar_width             Colorbar width (Default: 0.01)
  --colorbar_height            Colorbar height (Default: 0.2)
  --curve                      Plot curved style link (Default: OFF)
  --dpi                        Figure DPI (Default: 300)

[*] marker means the default value.

Examples

Example 1

Download example dataset:

Download four Erwinia phage genbank files

pgv-download-dataset -n erwinia_phage

Run CLI workflow:

pgv-mmseqs --gbk_resources MT939486.gbk MT939487.gbk MT939488.gbk LT960552.gbk \
           -o mmseqs_example1 --tick_style axis --align_type left --feature_plotstyle arrow

Example 2

Download example dataset:

Download four Erwinia phage genbank files

pgv-download-dataset -n erwinia_phage

Run CLI workflow:

Target range is specified (e.g. file:100-1000)

pgv-mmseqs --gbk_resources MT939486.gbk:250000-358115 MT939487.gbk:250000-355376 MT939488.gbk:250000-356948 LT960552.gbk:270000-340000 \
           -o mmseqs_example2 --tick_style bar --feature_plotstyle arrow

Example 3

Download example dataset:

Download six Enterobacteria phage genbank files

pgv-download-dataset -n enterobacteria_phage

Run CLI workflow:

pgv-mmseqs --gbk_resources NC_019724.gbk NC_024783.gbk NC_016566.gbk NC_013600.gbk NC_031081.gbk NC_028901.gbk \
           -o mmseqs_example3 --fig_track_height 0.7 --feature_linewidth 0.3 --tick_style bar --curve \
           --normal_link_color chocolate --inverted_link_color limegreen --feature_color skyblue