pymsaviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary

Keywords

bioinformatics genomics matplotlib msa multiple-sequence-alignment python sequence-alignment sequence-analysis visualization

Last synced: 4 months ago · JSON representation ·

Repository

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

Basic Info

Host: GitHub
Owner: moshi4
License: mit
Language: Python
Default Branch: main
Homepage: https://moshi4.github.io/pyMSAviz
Size: 7.2 MB

Statistics

Stars: 144
Watchers: 4
Forks: 17
Open Issues: 0
Releases: 9

Topics

bioinformatics genomics matplotlib msa multiple-sequence-alignment python sequence-alignment sequence-analysis visualization

Created about 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

pyMSAviz

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

```python from pymsaviz import MsaViz, getmsatestdata

msafile = getmsatestdata("HIGD2A.fa") mv = MsaViz(msafile, wraplength=60, showcount=True) mv.savefig("api_example01.png") ```

API Example 2

```python from pymsaviz import MsaViz, getmsatestdata

msafile = getmsatestdata("MRGPRG.fa") mv = MsaViz(msafile, colorscheme="Taylor", wraplength=80, showgrid=True, showconsensus=True) mv.savefig("api_example02.png") ```

API Example 3

```python from pymsaviz import MsaViz, getmsatestdata

msafile = getmsatestdata("MRGPRG.fa") mv = MsaViz(msafile, end=180, wraplength=60, showconsensus=True)

Extract MSA positions less than 50% consensus identity

posidentlessthan50 = [] identlist = mv.getconsensusidentitylist() for pos, ident in enumerate(identlist, 1): if ident <= 50: posidentlessthan50.append(pos)

Add markers

mv.addmarkers([1]) mv.addmarkers([10, 20], color="orange", marker="o") mv.addmarkers([30, (40, 50), 55], color="green", marker="+") mv.addmarkers(posidentlessthan50, marker="x", color="blue")

Add text annotations

mv.addtextannotation((76, 102), "Gap Region", textcolor="red", rangecolor="red") mv.addtextannotation((112, 123), "Gap Region", textcolor="green", rangecolor="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

Star History

Owner

Name: moshi
Login: moshi4
Kind: user

Repositories: 13
Profile: https://github.com/moshi4

Web Developer / Bioinformatics / GIS

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it as below.
authors:
  - family-names: Shimoyama
    given-names: Yuki
title: "pyMSAviz: MSA visualization python package for sequence analysis"
date-released: 2022-11-13
url: https://github.com/moshi4/pyMSAviz

GitHub Events

Total

Issues event: 3
Watch event: 54
Delete event: 1
Issue comment event: 2
Push event: 1
Fork event: 4
Create event: 1

Last Year

Issues event: 3
Watch event: 54
Delete event: 1
Issue comment event: 2
Push event: 1
Fork event: 4
Create event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 61
Total Committers: 1
Avg Commits per committer: 61.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 14
Committers: 1
Avg Commits per committer: 14.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
moshi	s**1@g**m	61

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 12
Total pull requests: 4
Average time to close issues: 13 days
Average time to close pull requests: 4 days
Total issue authors: 12
Total pull request authors: 2
Average comments per issue: 2.5
Average comments per pull request: 0.25
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 1
Average time to close issues: about 14 hours
Average time to close pull requests: 3 minutes
Issue authors: 4
Pull request authors: 1
Average comments per issue: 1.5
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

StefanoLonardi (1)
ahishsujay (1)
tonytony99 (1)
baozg (1)
thomashjordan (1)
Yogesh1-11 (1)
cx994 (1)
BadSpellign (1)
alejandrogzi (1)
heejongkim (1)
0xorial (1)
camilogarciabotero (1)

Pull Request Authors

moshi4 (3)
tvieijra (1)

Top Labels

Issue Labels

question (3) enhancement (2) wontfix (1) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 7,299 last-month

Total dependent packages: 2
Total dependent repositories: 0
Total versions: 9
Total maintainers: 1

pypi.org: pymsaviz

MSA visualization python package for sequence analysis

Documentation: https://pymsaviz.readthedocs.io/
License: mit
Latest release: 0.5.0
published over 1 year ago

Versions: 9
Dependent Packages: 2
Dependent Repositories: 0
Downloads: 7,299 Last month

Rankings

Dependent packages count: 6.6%

Downloads: 11.2%

Stargazers count: 12.7%

Forks count: 12.8%

Average: 14.8%

Dependent repos count: 30.6%

Maintainers (1)

moshi4

Last synced: 4 months ago

Dependencies

poetry.lock pypi

104 dependencies

pyproject.toml pypi

black ^22.10.0 develop
flake8 ^4.0.1 develop
ipykernel ^6.16.0 develop
mkdocs ^1.2 develop
mkdocs-jupyter ^0.21.0 develop
mkdocs-material ^8.2 develop
mkdocstrings 0.19.0 develop
pydocstyle ^6.1.1 develop
pytest ^7.2.0 develop
pytest-cov ^4.0.0 develop
biopython ^1.79
matplotlib ^3.5.2
python ^3.7.1

.github/workflows/ci.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/publish_mkdocs.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/publish_to_pypi.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

pymsaviz

Science Score: 44.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

pyMSAviz

Table of contents

Overview

Installation

API Usage

API Example

API Example 1

API Example 2

API Example 3

Extract MSA positions less than 50% consensus identity

Add markers

Add text annotations

CLI Usage

Basic Command

Options

CLI Example

CLI Example 1

CLI Example 2

CLI Example 3

Star History

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pymsaviz

Rankings

Maintainers (1)

Dependencies