Metadata-Version: 2.1
Name: cfutils
Version: 0.0.0.dev30
Summary: Chromatogram File Utils
Home-page: https://github.com/pypa/cfutils
Author: Ye Chang
Author-email: yech1990@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/pypa/cfutils/issues
Project-URL: Source, https://github.com/pypa/cfutils/
Description: # 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)
        
        code to generate demo above
        
        ```python
        import matplotlib.pyplot as plt
        from cfutils.parser import parse_abi, parse_fasta
        from cfutils.align import align
        from cfutils.show import highlight_base, plot_chromatograph
        
        query_record = parse_abi('./data/B5-M13R_B07.ab1', trim=False)
        subject_record = parse_fasta('./data/3kref.fa')
        mutations = align(query_record, subject_record, ignore_ambig=True)
        selected_mutation = mutations[5][2]
        print(selected_mutation)
        fig, ax = plt.subplots(1, 1, figsize=(15, 6))
        plot_chromatograph(
            query_record, ax, xlim=[selected_mutation - 10, selected_mutation + 10])
        highlight_base(selected_mutation, query_record, ax)
        plt.savefig('./test.pdf')
        ```
        
        ## How to install?
        
        ### form pypi
        
        *(use this way ONLY, if you don't know what't going on)*
        
        ```bash
        pip install cfutils
        ```
        
        ### manipulate the source code
        
        clone from github
        
        ```bash
        git clone git@github.com:yech1990/cfutils.git 
        ```
        
        install dependance
        
        ```bash
        make init
        ```
        
        do unittest
        
        ```bash
        make test
        ```
        
        ## How to use?
        
        in command line
        
        ```bash
        cfutils mut --query ./data/B5-M13R_B07.ab1 --subject data/3kref.fa
        ```
        
        as python modual
        
        ```python
        import cfutils as cf
        
        ```
        
        ## ChangeLog
        
        - build as python package for pypi
        - fix bug that highlihgting 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
        
Keywords: Utils Sanger Chromatogram
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: test
