pyMSAviz

Table of contents

• Overview
• Installation
• API Usage
• CLI Usage

Overview

pyMSAviz is a MSA(Multiple Sequence Alignment) visualization python package for sequence analysis implemented based on matplotlib. This package is developed for the purpose of easily and beautifully plotting MSA in Python. It also implements the functionality to add markers, text annotations, highlights to specific positions and ranges in MSA. pyMSAviz was developed inspired by Jalview and ggmsa. More detailed documentation is available here.

Fig.1 Simple visualization result

Fig.2 Customized visualization result

Installation

Python 3.9 or later is required for installation.

Install PyPI package:

pip install pymsaviz

Install bioconda package:

conda install -c conda-forge -c bioconda pymsaviz

API Usage

Only simple example usage is described in this section. For more details, please see Getting Started and API Docs.

API Example

API Example 1

from pymsaviz import MsaViz, get_msa_testdata

msa_file = get_msa_testdata("HIGD2A.fa")
mv = MsaViz(msa_file, wrap_length=60, show_count=True)
mv.savefig("api_example01.png")

API Example 2

from pymsaviz import MsaViz, get_msa_testdata

msa_file = get_msa_testdata("MRGPRG.fa")
mv = MsaViz(msa_file, color_scheme="Taylor", wrap_length=80, show_grid=True, show_consensus=True)
mv.savefig("api_example02.png")

API Example 3

from pymsaviz import MsaViz, get_msa_testdata

msa_file = get_msa_testdata("MRGPRG.fa")
mv = MsaViz(msa_file, end=180, wrap_length=60, show_consensus=True)

# Extract MSA positions less than 50% consensus identity
pos_ident_less_than_50 = []
ident_list = mv._get_consensus_identity_list()
for pos, ident in enumerate(ident_list, 1):
    if ident <= 50:
        pos_ident_less_than_50.append(pos)

# Add markers
mv.add_markers([1])
mv.add_markers([10, 20], color="orange", marker="o")
mv.add_markers([30, (40, 50), 55], color="green", marker="+")
mv.add_markers(pos_ident_less_than_50, marker="x", color="blue")
# Add text annotations
mv.add_text_annotation((76, 102), "Gap Region", text_color="red", range_color="red")
mv.add_text_annotation((112, 123), "Gap Region", text_color="green", range_color="green")

mv.savefig("api_example03.png")

CLI Usage

pyMSAviz provides simple MSA visualization CLI.

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']

CLI Example

Click here to download example MSA files.

CLI Example 1

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

CLI Example 2

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

CLI 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