seq-tools 🧬

What is it?

seq-tools is a Python package for biological sequence manipulation and NGS data filtration.

It can be used for:

• DNA, RNA, and Protein sequence processing (create reverse, complement, or reverse-complement counterparts for nucleic acids, as well as identification of trypsin cleavage sites in a protein).

• performing filtration of NGS reads in .fastq-files based on read length, GC content, and quality;

• сonverting a multi-line FASTA file (where sequence may be split across multiple lines) into a single-line FASTA file (where each sequence is stored on one line);

• parsing the standard BLAST output file (txt), extracting the description of the best match for each query.

It is an an educational project done as a part of Python course at the Bioinformatics institute (2025-2026 cohort).

Features

1. Sequence Classes

A class hierarchy with automated alphabet validation:

• DNASequence: Methods for reverse complement and transcription.

• RNASequence: Methods for RNA complementation.

• AminoAcidSequence: Trypsin cleavage site identification.

2. FASTQ Filter (filter_fastq function)

Filters FASTQ files using Biopython's FastqPhredIterator for iterative record processing without loading entire files into memory.

Argument	Default	Description
input_fastq	Required	Path to input FASTQ file.
output_fastq	Required	Output filename (saved in filtered/ directory).
gc_bounds	(0, 100)	Range (min, max) or upper threshold for GC content %.
length_bounds	(0, 2**32)	Range (min, max) or upper threshold for sequence length.
quality_threshold	0	Minimum mean Phred33 score per read.

3. Bio Files Processor

File format utilities:

• convert_multiline_fasta_to_oneline: Converts a multi-line FASTA file (where sequences are split across lines) into a single-line format.

• parse_blast_output: Parses a standard BLAST result file (.txt) to extract and sort the descriptions of the best matches (first hit) for each query.

Usage Example

from seqtools import DNASequence, AminoAcidSequence, filter_fastq
import bio_files_processor as bfp

# Sequence manipulation
dna = DNASequence("ATGGC")
print(dna.reverse_complement()) # GCCAT
print(dna.transcribe())         # RNASequence('AUGGC')

prot = AminoAcidSequence("MKKRRPL")
print(prot.trypsin_sites())     # [1, 2, 3]

# FASTQ Filter - retain only reads with GC content between 40% and 60%, no longer than 90 nucleotides and with average quality > 20
filtered_seqs = st.filter_fastq(
    input_fastq="data.fastq",
    output_fastq="clean_data.fastq" 
    gc_bounds=(40, 60),
    length_bounds = 90,
    quality_threshold=20
)

# Bio Files Processor
# Convert FASTA
bfp.convert_multiline_fasta_to_oneline("input_multiline.fasta", "output_oneline.fasta")

# Parse BLAST results
bfp.parse_blast_output("blast_results.txt", "sorted_descriptions.txt")

Project Structure

.
├── README.md
├── seqtools.py              # Sequence classes and FASTQ filter
└── bio_files_processor.py   # FASTA and BLAST utilities