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pgv-mmseqs

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.

pgv-mmseqs_example2.png

Installation

Conda

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

Pip

pip install pygenomeviz

Additional installation of MMseqs is required. On Ubuntu22.04 or later, MMseqs can be installed with apt command.

sudo apt install mmseqs2

Docker

docker run -it --rm -p 8501:8501 ghcr.io/moshi4/pygenomeviz:latest pgv-mmseqs -h

Usage

$ pgv-mmseqs --help
usage: pgv-mmseqs [options] seq1.gbk seq2.gbk seq3.gbk -o outdir

pyGenomeViz CLI workflow using MMseqs RBH method

positional arguments:
  seqs                    Input genbank files

General Options:
  -o , --outdir           Output directory
  --formats               Output image format ('png'[*],'jpg','svg','pdf',`html`[*])
  --reuse                 Reuse previous alignment result if available
  -q, --quiet             No print log on screen (default: OFF)
  -v, --version           Print version information
  -h, --help              Show this help message and exit

MMseqs Alignment Options:
  --threads               Threads number (Default: MaxThread - 1)
  --length_thr            Length threshold to be plotted (Default: 0)
  --identity_thr          Identity threshold to be plotted (Default: 0)
  --evalue_thr            E-value threshold to be plotted (Default: 1e-03)

Figure Appearence Options:
  --fig_width             Figure width (Default: 15)
  --fig_track_height      Figure track height (Default: 1.0)
  --track_align_type      Figure tracks align type ('left'|'center'[*]|'right')
  --feature_track_ratio   Feature track ratio (Default: 0.25)
  --show_scale_bar        Show scale bar (Default: OFF)
  --show_scale_xticks     Show scale xticks (Default: OFF)
  --curve                 Plot curved style link (Default: OFF)
  --dpi                   Figure DPI (Default: 300)
  --track_labelsize       Track label size (Default: 20)
  --scale_labelsize       Scale label size (Default: 15)
  --normal_link_color     Normal link color (Default: 'grey')
  --inverted_link_color   Inverted link color (Default: 'red')
  --segment_space         Track segment space ratio (Default: 0.02)
  --feature_type2color    Feature plot type & color (Default: ['CDS:orange'])
  --pseudo_color          Pseudo feature plot color (Default: 'lightgrey')
  --feature_plotstyle     Feature plot style ('[big]arrow'[*]|'[big]box'|'[big]rbox')
  --feature_linewidth     Feature line width (Default: 0.0)
  --feature_labeltrack    Feature label target track ('top'[*]|'all')
  --feature_labeltype     Feature label type ('product'|'gene'|'protein_id'|'None'[*])
  --feature_labelsize     Feature label size (Default: 8)
  --cbar_width            Colorbar width (Default: 0.01)
  --cbar_height           Colorbar height (Default: 0.2)

[*] marker means the default value.

Examples

Example 1

Download example dataset:

pgv-download acinetobacter_phage

Run CLI workflow:

pgv-mmseqs NC_049491.gbk NC_049492.gbk NC_049493.gbk NC_049494.gbk \
           -o pgv-mmseqs_example1 --track_align_type left --show_scale_xticks

pgv-mmseqs_example1.png

Example 2

Download example dataset:

pgv-download enterobacteria_phage

Run CLI workflow:

pgv-mmseqs NC_013600.gbk NC_016566.gbk NC_019724.gbk NC_024783.gbk NC_028901.gbk NC_031081.gbk \
           -o pgv-mmseqs_example2 --show_scale_bar --curve --feature_linewidth 0.3 \
           --feature_type2color CDS:skyblue --normal_link_color chocolate --inverted_link_color limegreen

pgv-mmseqs_example2.png

Example 3

Download example dataset:

pgv-download mycoplasma_mycoides

Run CLI workflow:

pgv-mmseqs GCF_000023685.1.gbff GCF_000800785.1.gbff GCF_000959055.1.gbff GCF_000959065.1.gbff \
           -o pgv-mmseqs_example3 --show_scale_bar --feature_type2color CDS:blue rRNA:lime

pgv-mmseqs_example3.png