cfutils 0.0.0.dev53

Chromatogram File Utils

/Users/yec/.local/share/nvim/site/pack/packer/opt/nvim-treesitter/parser/markdowcfutils

Chromatogram File Utils

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

Demo

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 [e-mail]: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