Basic Bioinf tools

This repository contains simple tools to perform basic operations with DNA/RNA sequences and FASTQ-format data.

Content

The script was made with Python 3.11.

Three modules are available now:

1. Toolbox for DNA and RNA operations (dna_rna_tools.py):

   • Input arguments must be strings. Needs at least one sequence to analyze and one procedure to run as last argument.
   • Performs one of the following procedures:
     • is_nucleic_acid: Check if sequence is nucleic acid.
     • transcribe: Perform transcription and reverse transcription of given sequence.
     • reverse: Reverse the sequence.
     • complement: Build complementary sequence.
     • reverse_complement: Build reversed complementary sequence.
   • Returns result of given procedure as list of strings, saves register of input sequences.

2. Improved tool for FASTQ format filtering (filter_fastq.py):

   • Input arguments must be in following format:
     • input_fastq (str): name of input file
     • output_fastq (str): name of output file
     • gc_bounds: Tuple[float, float] - bounds for filtering by GC percentage
     • length_bounds: Tuple[int, int] - bounds for filtering by length
     • quality_threshold: float - threshold for filtering by quality
   • Reads sequences in FASTQ format from file and filters by the given parameters.
   • Implemented functions:
     • compute_gc_content: Return GC percentage of given sequence.
     • quality_score: Return average quality score (Phred+33) of given sequence.
     • length_filter: Return names of reads filtered by length.
     • gc_filter:Return names of reads filtered by GC percentage.
     • quality_filter:Return names of reads with average quality above threshold.
     • filter_fastq:Return iterator(name, seq, qual).
   • Writes down the file 'output_fastq' in folder 'filtered' with overwrite protection.

3. New module io_fastq.py:

   • Implemented functions:
     • read_fastq: Read FASTQ file and make an iterator(name, seq, qual) for 'filter_fastq()'
     • write_fastq: Write iterator(name, seq, qual) to file after filtration.

Updates (05.10.2025)

*   Add global constants in modules
*   Rebuild `is_nucleic_acid` by reviewer's idea
*   Fix `transcribe`

Updates (12.10.2025)

*   Fix data types in function definitions
*   Fix repeating code in dna_rna_tools.py
*   Move filter_fastq() from main.py into filter_fastq.py
*   New run_filter_fastq() in main.py to operate filter_fastq.py quickly
*   Add module io_fastq to control file input and output for run_filter_fastq()
*   Small fixes in filter_fastq.py
*   Fix imports in main.py
*   Add new tool to work with FASTA format and BLAST output -> bio_files_processor.py
*   Add new function -> convert_multiline_fasta_to_oneline() in bio_files_processor.py

TODO

*   Add parse_blast_output() into bio_files_processor.py