SeqTools

SeqTools is a Python toolkit designed for working with nucleotide sequences. It provides essential functionality for DNA/RNA sequence operations, FASTQ filtering, and BLAST and FASTA files processing.

Features

• DNA/RNA Tools: Validate nucleotide sequences or perform operations like transcription, reverse, complement, and reverse_complement.
• Sequence Filtering: Filter FASTQ files by GC content, length, or base quality. Filtered file will be saved in 'filtered' subdirectory.
  • Filtering parameters are inclusive (e.g. gc_bounds=(40, 60) means that sequences with a GC content of 40% and 60% will also be included).
  • If only one number is provided for gc_bounds or length_bounds, it is treated as the upper threshold, with min defaulting to 0.
• Multi-line FASTA Conversion: Convert multi-line FASTA sequences to single-line format for easier downstream processing.
• BLAST Parsing: Extract the top-matched protein description for each query from BLAST text output and save a sorted protein list.

Installation

To use SeqTools, clone the repository:

git clone https://github.com/PenguinNell/SeqTools.git

Usage

Example 1: Using DNA/RNA tools

from seqtools import run_dna_rna_tools

result = run_dna_rna_tools('ATG', 'transcribe')
print(result)  # Output: 'AUG' (RNA sequence)

Example 2: Filtering FASTQ files

from seqtools import filter_fastq

filter_fastq(
    input_fastq="file.fastq",
    output_fastq="output_filtered.fastq",
    gc_bounds=(40, 60),
    length_bounds=(5, 10),
    quality_threshold=30
)
# Output: Filtered FASTQ file in 'filtered' subdirectory

Example 3: Converting Multi-line FASTA to One-line Format

from bio_files_processor import convert_multiline_fasta_to_oneline

convert_multiline_fasta_to_oneline('input.fasta', 'output_oneline.fasta')
# Output: Each sequence in 'output_oneline.fasta' will be in single-line format

Example 4: Parsing BLAST Output for Top Protein Hits

from bio_files_processor import parse_blast_output

parse_blast_output('results.txt', 'proteins.txt')
# Output: Each line in 'proteins.txt' contains the best protein match for each query, sorted alphabetically

Contact

For questions, suggestions, or contributions, please contact me at: ansycheva26@gmail.com