Chromatogram File Utils


Keywords
DNA, mutation, chromatogram, biology, bioinformatics, mutations, sanger-chromatograms
License
MIT
Install
pip install cfutils==0.0.0.dev52

Documentation

Readthedocs Build Status Pypi Releases Downloads

Chromatogram File Utils

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

Demo

plot chromatogram with mutation

command to generate the demo above

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)

pip install --user cfutils

manipulate the source code

  • clone from github
git clone git@github.com:y9c/cfutils.git
  • install the dependence
make init
  • do unittest
make test

How to use?

  • in the command line
cfutils mut --help
  • or as a python module
import cfutils as cf

ChangeLog

  • 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

  • change xaxis by peak location

  • fix bug that chromatogram switch pos after trim

  • 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