BioInf_Utilities

BioInf_Utilities is a set of Python utilities for working with biological sequences.

Project Structure

BioInf_Utilities/

├── main.py              # Main script (entry point)

├── README.md            # Documentation

└── modules/             # Functionality modules

    ├── dna_rna_tools.py    # DNA/RNA utilities

    ├── bio_files_processor.py # Bioinformatic file format utilities

    └── fastq_utils.py      # FASTQ processing

Installation

git clone (https://github.com/rentagr/BioInf_Utilities.git)

cd BioInf_Utilities

Usage

DNA/RNA Sequence Tools

#from modules.dna_rna_tools import run_dna_rna_tools

Check if sequence is valid nucleic acid

result = run_dna_rna_tools("ATCG", "is_nucleic_acid")

Transcribe DNA to RNA

result = run_dna_rna_tools("ATCG", "transcribe")

Get reverse complement

result = run_dna_rna_tools("ATCG", "reverse_complement")

Multiple sequences at once

results = run_dna_rna_tools("ATCG", "AUCG", "reverse")

FASTQ Processing

For file-based processing:

from modules.fastq_utils import filter_fastq_file

Filter FASTQ files by GC content, length and quality

filter_fastq_file(
    "input.fastq",
    "filtered/output.fastq", 
    gc_bounds=(40, 60),
    length_bounds=(50, 150),
    quality_threshold=20
)

For dictionary-based processing:

from modules.fastq_utils import filter_fastq_dict

sequences = {
    'read1': ('ATCG', 'IIII'),
    'read2': ('GGCC', '!!!!')
}

filtered = filter_fastq_dict(
    sequences,
    gc_bounds=(20, 80),
    length_bounds=(50, 150), 
    quality_threshold=20
)

Bioinformatics File Processing

from bio_files_processor import convert_multiline_fasta_to_oneline, parse_blast_output

Convert multi-line FASTA to single-line format

convert_multiline_fasta_to_oneline("input.fasta", "output.fasta")

Parse BLAST results and extract best matches

parse_blast_output("blast_results.txt", "best_matches.txt")

Available Functions

DNA/RNA Tools Module

• is_nucleic_acid() - Validate DNA/RNA sequences
• transcribe() - Transcribe between DNA and RNA
• reverse() - Reverse sequences
• complement() - Get complementary sequences
• reverse_complement() - Get reverse complement
• run_dna_rna_tools() - Main interface for DNA/RNA operations

FASTQ Utilities Module

• validate_fastq_record() - Validate FASTQ format and characters
• calculate_gc_content() - Calculate GC percentage
• calculate_average_quality() - Calculate average Phred quality
• filter_fastq_dict() - Filter sequence dictionaries by criteria
• filter_fastq_file() - Filter FASTQ files (reads and writes files)
• read_fastq_file() - Read FASTQ files into dictionary format
• write_fastq_file() - Write sequences to FASTQ files

Bio Files Processor Module

• convert_multiline_fasta_to_oneline() - Convert multi-line FASTA to single-line
• parse_blast_output() - Extract best matches from BLAST results

Documentation

Full function documentation is available through built-in docstrings:

from main import filter_fastq
help(filter_fastq)

All functions have type annotations and docstrings.

Dependencies

• Python 3.6+
• No external dependencies required

Contacts

For questions and suggestions:

Email: renata.tag.isl@gmail.com

BioInf_Utilities was developed as part of an educational Bioinformatics Institute project