TransDNA

Install

Install for training

• Clone the repo

git clone https://github.com/qinyunnn/TransDNA.git

• Install Conda: please see https://docs.conda.io/en/latest/miniconda.html
• Create Conda env:

conda create -n TransDNA python==3.8
conda activate TransDNA
pip install -r requirements.txt

Usage

We provided a training example in examples.

Data Preparation

# put your dataset under data/ directory with the same structure shown in the example/data/

data
  source_data
    |-reads.txt
    |-reference.txt
  target_data
    |-reads.txt
    |-reference.txt

Notices:

• In reads.txt, the adjacent two clusters are segmented using '==============================='. For example:

AACCAATACCTTGAACCTAACTCGAGTTAACAAACGCAATTCACAGAACAAGGACGTCGGACGGTGTCCAGAATACCGGCCTCGTGACCGTGGCCAGGGAACCTGACAATGTCAGGCCTTACCGACACACGCAACCTCTTGCTGAAAGGCCT
AACCAATACCTTGAACCTAACTCGAGTTAACAAACGCAATTCACAGAACAAGGACGTCGGACGGTGTCCAGAATACCGGCCTCGTGACCGTGGCCAGGGAACCTGACAATGTCAGGCCTTACCGACAACGCAACCTCTTGCTGAAAGGCCT
AACCAATACCTTGAACCTAACTCGAGTTAACAAACGCAATTCACAGAACAAGGACGTCGGACGGTGTCCAGAATACCGGCCTCGTGACCGTGGCCAGGGAACCTGACAATGTCAGGCCTTACCGACACACGCAACCTCTTGCTGAAAGGCCT
AACCAATACCTTGAACCTAACTCGAGTTAACAAACGCAATTCACAGAACAAGGACGTCGGACGGTGTCCAGAATACCGGCCTCGTGACCGTGGCCAGGGAACCTGACAATGTCAGGCCTTACCGACACACGCAACCTCTTGCTGAAAGGCCT
===============================
AATACCTTGAAGTCACTGGTACTGAACATGCCTTCTGACCGTTAGGACTTATCTTCCTGTCGGTATAAGATCTACTACTACAACACTGGTTTCAACTAGCGGGAGAAGTCCTTACCGAGTTCTGCGGCTGGCTGATAGCGTGTGCCCTCTGG
AATACCTTGAAGTCACTGGTACTGAACATGCCTTCTGACCGTTAGGACTTATCTTCCTGTCGGTATAAGATCTACTACTACAACACTGGTTTCAACTAGCGGGAGAAGTCCTTACCGAGTTCTGCGGCTGGCTGATAGCGTGTGCCCTCTGG
AATACCTTGAAGTCACTGGTACTGAACATGCCTTCTGACCGTTAGGACTTATCTTCCTGTCGGTATAAGATCTACTACTACAACACTGGTTTCAACTAGCGGGAGAAGTCCTTACCGAGTTCTGCGGCTGGCTGATAGCGTGTGCCCTCTGG
===============================

Run

• First, you can train the source domain with run_source.sh to obtain the pre-trained encoder and decoder.

    cd examples
    bash run_source.sh

• Then, transfer learning is performed using run_target.sh.

    bash run_target.sh

You can change running parameters in run_source.sh and run_target.sh.