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pgv-pmauve CLI Document

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.

pmauve_example1.png

Installation

Additional installation of progressiveMauve is required.

Conda

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

Pip (Ubuntu)

pip install pygenomeviz

In Ubuntu, progressiveMauve can be installed with apt command below.

sudo apt install progressivemauve

Usage

Basic Command

pgv-pmauve --seq_files seq1.gbk seq2.gbk seq3.gbk seq4.gbk -o pmauve_example

Options

General Options:
  --seq_files IN [IN ...]  Input genome sequence files (Genbank or Fasta format)
  -o OUT, --outdir OUT     Output directory
  --refid                  Reference genome index (Default: 0)
  --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

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: 'tomato')
  --align_type             Figure tracks align type ('left'|'center'[*]|'right')
  --tick_style             Tick style ('bar'|'axis'|None[*])
  --plotstyle              Block box plot style ('box'[*]|'bigbox')
  --cmap                   Block box colormap (Default: 'hsv')
  --curve                  Plot curved style link (Default: OFF)
  --dpi                    Figure DPI (Default: 300)

[*] marker means the default value.
Colormap(--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:

Download four E.coli genbank files

pgv-download-dataset -n escherichia_coli

Run CLI workflow:

pgv-pmauve --seq_files NC_000913.gbk NC_002695.gbk NC_011751.gbk NC_011750.gbk \
           -o pmauve_example1 --tick_style bar

pmauve_example1.png

pmauve_example1/result.png

Example 2

Download example dataset:

Download six M.gallisepticum genbank files

pgv-download-dataset -n mycoplasma_gallisepticum

Run CLI workflow:

pgv-pmauve --seq_files NC_004829.gbk NC_017502.gbk NC_017503.gbk NC_018407.gbk NC_018408.gbk NC_018409.gbk \
           -o pmauve_example2 --fig_track_height 0.7 --align_type left --cmap viridis --tick_style axis --curve

pmauve_example2.png

pmauve_example2/result.png