ljmu_masters_dissertation's Introduction

Application of ML for DRP using WGS data on MTB genomes.

This repository contains the code for my masters dissertation.

To execute the code, the following execution environments are recommended.

AWS/Azure Batch for genomic pre-processing.
Azure ML Studio for notebooks, with a decent server.

The rest of the instructions are embedded within the notebooks/FINAL/*ipynb notebooks.

Project Organization

├── LICENSE
├── README.md
│
├── conda_enviroment.yml <- The minimal conda file needed to recreate the environment.
├── azure_enviroment.yml <- The conda file for the Azure ML studio.
│
├── data
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for modeling.
│   └── raw            <- The original, immutable data dump.
│
├── models             
│      ├── ALL_FEATURES   <- Models trained on All features.
│      │      ├── FINAL   
│      │
│      └── PCA300         <- Models trained on PCA300 features.
│
├── notebooks          
│   ├── FINAL          <- The final jupyter notebooks, named as per their execution order.
│      └── 001_feature_engineering.ipynb
│      └── 002_choose_limited_tbportals_genomes.ipynb <- Contains the SRA IDs of genomes, can be downloaded through download.nf
│      └── 003_eda_mono_resistance.ipynb
│      └── 004_model_grids.ipynb
│      └── 005_stacked_ensemble.ipynb
│      └── 006_pca_based_ml.ipynb
│      └── 007_model_inspection_with_without_pca.ipynb
│
├── src                
│   ├── genomic_preprocessing           <- Scripts for genomic pre-processing
│      └── nyu_gatk.sh
│      └── download.nf
│      └── bwa.nf
│      └── fastqc.nf
│      └── gatk.nf
│      └── picard.nf
│      └── samtools.nf
│      └── tb_profiler.nf
│      └── trimmomatic.nf
│   
│   
│   ├── features       <- Scripts to turn raw VCF data into tabular data for modeling
│       └── 01_tbprofiler.py
│       └── 02_vcf_drop_cols.py
│       └── 03_filter_unique_snps.py
│       └── 04_binarize_vcf.py
│       └── 05_final_snp_df.py

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