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Development Approach

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Robert J. Gifford edited this page Jun 25, 2024 · 2 revisions

The DIGS tool is developed using Object Oriented Perl (OOPERL). This reflects my postdoctoral research experience working with the Stanford HIV Drug Resistance Database (HIVdb). The HIVdb code I worked with, which was written by Bradley Betts using OOPERL, introduced me to this style. Since the first Perl programs I worked with were in OOPERL, and I was previously familiar with object-oriented concepts from some dabbling in C++, OOPERL became my default approach, but I have mainly used it only as a framework for compartmentalizing related functions. My code doesn’t fully utilize OO features like polymorphism.

  • Rob Gifford, DIGS Tool developer.

The Database Integrated Genome Screening (DIGS) Tool Wiki

Maintained by: R.J. Gifford.

DIGS Tool

  1. Home
  2. Background
  3. Requirements
  4. Installation
  5. Getting Started

Overview

  1. DIGS Concept
  2. Investigation Structure
  3. Exploration Phase
  4. Analysis Phase

Input Components

  1. Target Database (tDB)
  2. Reference Sequence Library (RSL)
  3. Query Sequences (Probes)
  4. Control File

Process

  1. Running a Screen
  2. Project Database
  3. Database Querying
  4. Extending the Project DB Schema
  5. Reclassifying Results
  6. Merging Contiguous Hits

Reference

  1. Example SQL
  2. Archive & Restore Project DBs

Further Information

  1. FAQ
  2. NCBI taxonomy DB
  3. Installation-Guide-for-OS-X

Source Code

  1. Development Approach
  2. Code Summary
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