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Chromatogram File Utils

Project description

cfutils

Chromatogram File Utils

for sanger sequencing data visualizing, alignment, mutation calling, and trimming etc.

Demo

plot chromatogram with mutation

code to generate demo above

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)

pip install cfutils

manipulate the source code

clone from github

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

install dependance

make init

do unittest

make test

How to use?

in command line

cfutils mut --query ./data/B5-M13R_B07.ab1 --subject data/3kref.fa

as python modual

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

Project details


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