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pymsaviz CLI Document

Usage

Basic Command

pymsaviz -i [MSA file] -o [MSA visualization file]

Options

$ pymsaviz --help
usage: pymsaviz [options] -i msa.fa -o msa_viz.png

MSA(Multiple Sequence Alignment) visualization CLI tool

optional arguments:
  -i I, --infile I    Input MSA file
  -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
  --format            MSA file format (Default: 'fasta')
  --color_scheme      Color scheme (Default: 'Zappo')
  --start             Start position of MSA visualization (Default: 1)
  --end               End position of MSA visualization (Default: 'MSA Length')
  --wrap_length       Wrap length (Default: None)
  --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
  --label_type        Label type ('id'[default]|'description')
  --show_grid         Show grid (Default: OFF)
  --show_count        Show seq char count without gap on right side (Default: OFF)
  --show_consensus    Show consensus sequence (Default: OFF)
  --consensus_color   Consensus identity bar color (Default: '#1f77b4')
  --consensus_size    Consensus identity bar height size (Default: 2.0)
  --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
  --dpi               Figure DPI (Default: 300)
  -v, --version       Print version information
  -h, --help          Show this help message and exit

Available Color Schemes:
['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']

Example Command

Click here to download example MSA files.

Example 1

pymsaviz -i ./example/HIGD2A.fa -o cli_example01.png --color_scheme Identity

example01.png

Example 2

pymsaviz -i ./example/MRGPRG.fa -o cli_example02.png --wrap_length 80 \
         --color_scheme Taylor --show_consensus --show_count

example02.png

Example 3

pymsaviz -i ./example/MRGPRG.fa -o cli_example03.png --start 100 --end 160 \
         --color_scheme Flower --show_grid --show_consensus --consensus_color tomato

example03.png