https://github.com/y9c/cfutils

🧬 Chromatogram File Utils, a package that integrates trace visualization, mutation calling and quality control for Sanger sequencing data.
https://github.com/y9c/cfutils

bioinformatics biology mutations sanger-chromatograms

Last synced: 5 months ago
JSON representation

🧬 Chromatogram File Utils, a package that integrates trace visualization, mutation calling and quality control for Sanger sequencing data.

• Host: GitHub
• URL: https://github.com/y9c/cfutils
• Owner: y9c
• Created: 2018-05-13T06:26:26.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-11-30T08:16:37.000Z (10 months ago)
• Last Synced: 2025-04-06T17:18:07.804Z (6 months ago)
• Topics: bioinformatics, biology, mutations, sanger-chromatograms
• Language: Python
• Homepage: https://cfutils.yech.science/
• Size: 15.8 MB
• Stars: 22
• Watchers: 1
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Funding: .github/FUNDING.yml

Awesome Lists containing this project

README

          
[![Readthedocs](https://readthedocs.org/projects/cfutils/badge/?version=latest)](https://cfutils.readthedocs.io/en/latest/?badge=latest)

[![Pypi Releases](https://img.shields.io/pypi/v/cfutils.svg)](https://pypi.python.org/pypi/cfutils)

[![Downloads](https://static.pepy.tech/badge/cfutils)](https://pepy.tech/project/cfutils)

**Chromatogram File Utils**

For Sanger sequencing data visualizing, alignment, mutation calling, and trimming etc.

## Demo

![plot chromatogram with mutation](https://raw.githubusercontent.com/y9c/cfutils/master/data/plot.png)

> command to generate the demo above

```bash

cfutils mut --query ./data/B5-M13R_B07.ab1 --subject ./data/ref.fa --outdir ./data/ --plot

```

## How to use?

- You can have mutation detection and visualization in one step using the command line.

```bash

cfutils mut --help

```

- You can also integrate the result matplotlib figures and use it as a python module.

An example:

```python

import matplotlib.pyplot as plt

import numpy as np

from cfutils.parser import parse_abi

from cfutils.show import plot_chromatograph

seq = parse_abi("./data/B5-M13R_B07.ab1")

peaks = seq.annotations["peak positions"][100:131]

fig, axes = plt.subplots(2, 1, figsize=(12, 6), sharex=True)

plot_chromatograph(

    seq,

    region=(100, 130),

    ax=axes[0],

    show_bases=True,

    show_positions=True,

    color_map=dict(zip("ATGC", ["C0", "C2", "C1", "C4"])),

)

axes[1].bar(peaks, np.random.randn(len(peaks)), color="0.66")

plt.show()

```

![plot chromatogram in_matplotlib](https://raw.githubusercontent.com/y9c/cfutils/master/data/matplotlib_example.png)

## How to install?

### form pypi

_(use this way ONLY, if you don't know what's going on)_

```bash

pip install --user cfutils

```

### manipulate the source code

- clone from github

```bash

git clone git@github.com:y9c/cfutils.git

```

- install the dependence

```bash

make init

```

- do unittest

```bash

make test

```

## ChangeLog

- Reverse completement the chromatogram file. (Inspired by Snapgene)

- build as python package for pypi

- fix bug that highlighting wrong base

- replace blastn with buildin python aligner

## TODO

- [ ] call mutation by alignment and plot Chromatogram graphic

- [ ] add a doc

- [x] change xaxis by peak location

- [ ] fix bug that chromatogram switch pos after trim

- [x] wrap as a cli app

- [ ] return quality score in output

- [ ] fix issue that selected base is not in the middle

- [ ] fix plot_chromatograph rendering bug

- [ ] add projection feature to make align and assemble possible