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pgv-pmauve

pgv-pmauve is one of the CLI workflows in pyGenomeViz for visualization of genome alignment results using progressiveMauve. It can be used to visualize commonly conserved regions between all genomes.

pgv-pmauve_example1.png

Installation

Conda

conda install -c conda-forge -c bioconda pygenomeviz progressivemauve

Pip

pip install pygenomeviz

Additional installation of progressiveMauve is required. On Ubuntu, progressiveMauve can be installed with apt command.

sudo apt install progressivemauve

Docker

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

Usage

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

pyGenomeViz CLI workflow using progressiveMauve

positional arguments:
  seqs                    Input genbank or fasta 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

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')
  --refid                 Reference genome index (Default: 0)
  --block_plotstyle       Synteny block plot style ('box'[*]|'bigbox')
  --block_cmap            Synteny block colormap (Default: 'gist_rainbow')

[*] marker means the default value.

Multi Contigs Input Case

progressiveMauve cannot align for multiple contigs. Therefore, when multiple contigs are included in the input, a sequence that concatenates the multiple contigs into one is used as the input.

Colormap(--block_cmap) Option

User can arbitrarily choose the visualization colormap from the various colormap types in matplotlib.
See Choosing Colormaps in Matplotlib for details.

Examples

Example 1

Download example dataset:

pgv-download escherichia_coli

Run CLI workflow:

pgv-pmauve NC_000913.gbk.gz NC_002695.gbk.gz NC_011751.gbk.gz NC_011750.gbk.gz \
           -o pgv-pmauve_example1 --show_scale_bar

pgv-pmauve_example1.png

Example 2

Download example dataset:

pgv-download mycoplasma_mycoides

Run CLI workflow:

pgv-pmauve GCF_000023685.1.gbff GCF_000800785.1.gbff GCF_000959055.1.gbff GCF_000959065.1.gbff \
           -o pgv-pmauve_example2 --feature_track_ratio 0.15 --block_cmap viridis --track_align_type left \
           --show_scale_xticks --curve

pgv-pmauve_example2.png