Metadata-Version: 2.1
Name: cfutils
Version: 0.0.0.dev52
Summary: Chromatogram File Utils
Home-page: https://github.com/yech1990/cfutils
License: MIT
Keywords: DNA,mutation,chromatogram,biology
Author: Ye Chang
Author-email: yech1990@gmail.com
Requires-Python: >=3.8,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Requires-Dist: Click (>=7.0.0,<8.0.0)
Requires-Dist: biopython (>=1.70,<2.0)
Requires-Dist: matplotlib (>=3.0.0,<4.0.0)
Project-URL: Documentation, https://cf.readthedocs.io/
Project-URL: Repository, https://github.com/yech1990/cfutils
Description-Content-Type: text/markdown

# cfutils

**Chromatogram File Utils**

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

## Demo

![plot chromatogram with mutation](https://raw.githubusercontent.com/yech1990/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 install?

### form pypi

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

```bash
pip install cfutils
```

### manipulate the source code

- clone from github

```bash
git clone git@github.com:yech1990/cfutils.git 
```

- install the dependence

```bash
make init
```

- do unittest

```bash
make test
```

## How to use?

- in the command line

```bash
cfutils mut --help
```

- or as a python module

```python
import cfutils as cf
```

## ChangeLog

- build as python package for pypi
- fix bug that highlighting wrong base

## 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   

