Applied Programming for Bioinformatics

Solutions and final project for the APBI course at the University of Vienna (SS17).

This repository contains exercises from the course 2017S 300353-1 Applied Programming for Bioinformatics — a practical introduction to programming for solving biological problems, with a focus on text processing and automation of external tools — as well as the final project: an orthologous group analysis using the eggNOG v4 database.

Note: This repo was updated in 2026 with Hermes Agent to test AI-assisted repository maintenance. The original content and structure have been preserved.

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Repository Structure

AppliedProgrammingBioinfo/
├── weekly_exercises/
│   ├── 01_Basics/            Perl — basic syntax, file I/O, sequence handling
│   ├── 02_Subroutines/       Perl — string manipulation, pattern matching
│   ├── 03_FileIO/            Perl — subroutines, arrays, hash tables
│   ├── 04_CommandLine/       Perl — command-line arguments
│   ├── 05_Modules/           Perl — restriction enzyme analysis (Pattern.pm, Restrictions.pm)
│   ├── 06_Databases/         Perl — SQL database queries via DBI
│   ├── 07_Python_Basics/     Python — sequence analysis, file parsing
│   ├── 08_Python_Patterns/   Python — pattern search, restriction site analysis
│   └── 09_Bash/              Bash — shell scripting, automation
├── final_project/            ← Final project (eggNOG orthology analysis)
│   ├── orthologe_comparison.pl
│   ├── taxonomic_distribution.pl
│   ├── rodent_gene_isolation.pl
│   ├── runscript.sh
│   ├── lib/
│   │   └── FinalProject.pm   ← Shared Perl module (taxon lookup, counting, descriptions)
│   └── data/
│       ├── eggnog4.functional_categories.txt
│       └── eggnog4.species_list.txt
├── python_rewrite/           ← Partial Python port of the Perl exercises (unfinished)
│   ├── Exercise01_01.py .. 03_04.py
│   └── ABANDONED.md
├── example_data/             ← Shared datasets used by multiple exercises
│   ├── gene_positions1.txt
│   ├── gene_positions2.txt
│   ├── names.txt
│   ├── sequence.fasta
│   └── swissprot_list.txt
├── perl_cheat_sheet.txt      ← Common Perl pitfalls reference
├── README.md
├── LICENSE
└── .gitignore

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Weekly Exercises

9 weekly assignments progressing from Perl basics through Python to Bash scripting.

Exercise	Language	Topic
01	Perl	Basic syntax, file I/O, sequence handling
02	Perl	String manipulation, pattern matching
03	Perl	Subroutines, arrays, hash tables
04	Perl	Regular expressions (contributed by a friend — not uploaded)
05	Perl	Restriction enzyme analysis
06	Perl	SQL database queries
07	Python	Sequence analysis, file parsing
08	Python	Pattern search, restriction site analysis
09	Bash	Shell scripting, automation

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Final Project — eggNOG Orthology Analysis

The final_project/ directory contains the capstone project for the course (originally in a separate repository). It analyses orthologous groups from the eggNOG v4 database across multiple species.

Pipeline

The project consists of three Perl scripts orchestrated by a Bash wrapper:

1. orthologe_comparison.pl — given two species, counts orthologous groups they share and genes from species 1 that have a homolog in species 2

2. taxonomic_distribution.pl — given three species, identifies genes from species 1 that have a homolog in species 3 but not in species 2 (lineage-specific gene loss)

3. rodent_gene_isolation.pl — given one species, identifies orthologous groups that only contain genes from that species (species-specific orthogroups)

4. runscript.sh — interactive orchestrator that chains all three scripts, prompts for species names, and warns about output file conflicts

Shared Module

lib/FinalProject.pm provides four subroutines used across all scripts:

• get_taxon_ID() — looks up a species name → NCBI taxon ID
• gene_count_members() — counts gene occurrences for a taxon across orthologous groups
• get_protein_ID() — extracts protein IDs from eggNOG members files
• get_desc() — cross-references COG functional category codes (e.g. J → "Translation") with eggNOG descriptions

Data Dependencies

The pipeline uses eggNOG v4 data files:

• meNOG.members.tsv — the orthologous group membership file (not shipped due to size — must be downloaded from eggNOG)
• eggnog4.functional_categories.txt — COG functional category descriptions
• eggnog4.species_list.txt — species-to-taxon-ID mapping

How to Run

cd final_project

# Interactive mode (prompts for species names)
bash runscript.sh

# Direct mode (pass species as command-line arguments)
perl orthologe_comparison.pl "Homo sapiens" "Mus musculus"
perl taxonomic_distribution.pl "Homo sapiens" "Mus musculus" "Pan troglodytes"
perl rodent_gene_isolation.pl "Mus musculus"

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Structure Notes

• The first six exercises are written in Perl (developed with Eclipse + EPIC plugin on Windows/Linux).
• Exercises 7–8 are written in Python (developed with PyCharm).
• Exercise 09 covers Bash scripting (developed on Fedora/KDE and Windows Subsystem for Linux).
• Exercise 04 (regex) was contributed by a friend and is not included here.
• A cheat sheet with common Perl pitfalls is included as perl_cheat_sheet.txt.

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License

This project is licensed under the MIT License — see the LICENSE file for details.