Bioinf-utilities

A set of tools for working with biological sequences, including DNA/RNA analysis and FASTQ file filtering.

Installation

1. Clone the repository:

git clone git@github.com:a-v-kolos/Bioinf-utilities.git

2. Make sure you have Python 3.6 or higher installed.

Supported operations:

1. The main function run_dna_rna_tools() takes sequences and an operation:

• is_nucleic_acid - nucleic acid validation

• transcribe - DNA→RNA transcription

• reverse - sequence reversal

• complement - complementary sequence

• reverse_complement - reverse-complementary sequence

2. The filter_fastq() function filters sequences by GC content, length, and quality:

• gc_bounds: GC content range in (default: 0-100)

• length_bounds: sequence length range (default: 0-2³²)

• quality_threshold: minimum average read quality (phred33)

Modules

dna_rna_modules.py Contains functions for nucleic acid manipulation:

• is_nucleic_acid(seq) - checks if sequence is DNA or RNA

• transcribe(seq) - transcribes DNA to RNA

• reverse(seq) - returns reversed sequence

• complement(seq) - returns complementary sequence

• reverse_complement(seq) - returns reverse-complementary sequence

filter_fastq_modules.py Contains helper functions for FASTQ filtering:

• calculate_gc_content(seq) - calculates GC content

• calculate_average_quality(quality_string) - calculates average read quality

• check(value, bounds) - checks if value is within specified bounds

bio_files_processor.py Contains utility functions for processing bioinformatics file formats:

parse_blast_output(input_file: str, output_file: str) -> None - extracts the best protein matches from BLAST results and saves them to a sorted list

convert_multiline_fasta_to_oneline(input_fasta: str, output_fasta: str | None = None) -> None - converts a FASTA file with multiline sequences to a format where each sequence is contained in a single line