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 use?

• You can have mutation detection and visualization in one step using the command line.

cfutils mut --help

• You can also integrate the result matplotlib figures and use it as a python module.

An example:

import matplotlib.pyplot as plt
import numpy as np

from cfutils.parser import parse_abi
from cfutils.show import plot_chromatograph

seq = parse_abi("./data/B5-M13R_B07.ab1")
peaks = seq.annotations["peak positions"][100:131]

fig, axes = plt.subplots(2, 1, figsize=(12, 6), sharex=True)
plot_chromatograph(
    seq,
    region=(100, 130),
    ax=axes[0],
    show_bases=True,
    show_positions=True,
    color_map=dict(zip("ATGC", ["C0", "C2", "C1", "C4"])),
)
axes[1].bar(peaks, np.random.randn(len(peaks)), color="0.66")
plt.show()

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 [email protected]:y9c/cfutils.git

• install the dependence

make init

• do unittest

make test

ChangeLog

• Reverse completement the chromatogram file. (Inspired by Snapgene)
• 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