Bioinformatics_utilities

This repository contains homework scripts developed in the Python course at the Bioinformatics Institute during the 2023-2024 academic year. Code with examples in the showcases.py notebook is marked with *.

bioseq.py

This script provides various functionalities for working with biological data.

• RNASequence/DNASequence/AminoAcidSequence classes *

Assists in working with DNA, RNA, and amino acid sequencing data.

• filter_fastq function

Filters FASTQ files based on GC content, sequence length, and quality threshold.

• run_genscan function *

Uses the Genscan prediction tool for DNA sequences, and extracts predicted peptide sequences, intron, and exon information.

• telegram_logger decorator

Sends messages and log files of run scripts to a Telegram chat for notification purposes. Implementation of this function was based on Telegram bot API.

bio_files_processor.py

• convert_multiline_fasta_to_oneline function

Converts any number of DNA/RNA/protein sequences in FASTA file from multi-line FASTA files into one-line FASTA format.

• OpenFasta context manager *

Opens FASTA files, like the open built-in function. Returns separate FASTA records including ID, description, and sequence.

custom_random_forest.py

• RandomForestClassifierCustom class *

Allows to apply parallelization for custom random forest class for faster usage

test_modules.py

Contains tests to verify the functionality of the code in bioseq.py and bio_files_processor.py

showcases.py

Demonstrates examples of using functions and classes from other files in the repository.