This repository contains homeworks completed as part of the Python course during the annual retraining program at the Bioinformatics Institute (2023/2024). The required third-party dependencies are listed in the requirements.txt.

Topics covered: basic and advanced Python syntax, functions, working with files, OOP, API and web page parsing, code testing.

Below is a brief description of the module:

🌿 bi_python_kit.py

• filter_fastq

Biopython-based FASTQ records filter working according to the specified criteria.

• BiologicalSequence

OOP-based class that allows to perform simple operations with biological sequences (DNA, RNA, amino acid sequences).

• telegram_logger

Decorator for logging function execution and sending logs to Telegram bot. It is written without using libraries that automate the creation of a Telegram bot.

• GenscanOutput

Python API for http://hollywood.mit.edu/GENSCAN.html. Represents the output of the GENSCAN prediction.

🌿 bio_file_processor.py

• convert_multiline_fasta_to_oneline

Function for conversion of multi-line FASTA sequences to single-line sequences.

• select_genes_from_gbk_to_fasta

Function that selects neighbor genes for the gene of interest from the GBK file and writes their protein sequences into FASTA format.

• OpenFasta

Context manager for reading FASTA files.

🌿 custom_random_forest.py

• RandomForestClassifierCustom

Class for custom implementation of a Random Forest classifier. It uses thread parallelization to get results faster.

🌿 test_script_pytest.py

A set of tests using the pytest library that checks the correct execution of some module functions.

🌿 Showcases.ipynb

Contains selected examples of how this module works.