Chromosomal Structure Tools

ShRec3D algorithm in Python3 and Predicted Chromosomal Structure Visualizer.

Introduction

ShRec3D

Implementation of the algorithm described in 3D genome reconstruction from chromosomal contacts.

Preview

Data From test/data/sparseMat_Normalized.metrics

With Difference Argument.

1. -s 0.1 -m -b
2. -s 0.1
3. -s 1.0 -m -b
4. -s 1.0

Usage

Requirements

1. python3
2. python package in requirements.txt
3. ffmpeg (Optional)

FullSizeMatrix_Generator

Used to Generate Full Size Matrix.

usage: FullSizeMatrix_Generator [-h] -f F -o O

optional arguments:
  -h, --help  show this help message and exit
  -f F        Path to Original Hi-C Normalized Sparse Matrix File.
  -o O        Path to Output of Full Size Matrix(CSV).

ExamPle:

python3 -u src/FullSizeMatrix_Generator.py -f test/data/sparseMat_Normalized.metrics -o out/mat.csv

Coordinates_Calculation

Used to Generate Coordinates Matrix.

usage: Coordinates_Calculation [-h] -f F -o O
ExamPle: 

optional arguments:
  -h, --help  show this help message and exit
  -f F        Path to Normalized Full Size Matrix(CSV).
  -o O        Path to Output(CSV).

ExamPle:

python3 -u src/Coordinates_Calculation.py -f out/mat.csv -o out/Coord.csv

Visualizer

Used to Visualize chromosomal Structure.

usage: Visualizer [-h] -f F -o O -t T [-s S]

optional arguments:
  -h, --help  show this help message and exit
  -f F        Path to coordinates File(csv).
  -o O        Path to Output(SVG).
  -t T        Title of Image.
  -s S        Smooth Factor(Default: 1.0). May be 0.1, 1.0, 2.0,
  -b          Line With Black Border.
  -m          Line End With Marker.

It is Better to use -b and -m simultaneously, or not to use simultaneously.

ExamPle:

python3 -u src/Visualizer.py -f out/Coord.csv -o out/out.svg -t chromosomal_No_1 -b -m

CopyRight Note

The Original implementation of the algorithm is from kpj/ShRec3D.