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.
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
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