seq-miner 1.3.0

A command-line tool to extract and filter sequence reads from BAM and FASTQ files by ID, quality score, and length.

seq-miner

seq-miner is a lightweight tool to extract and filter reads from BAM or FASTQ files based on:

• Specific read IDs
• Mean quality score threshold
• Minimum read length
• Multi-threading (FASTQ)
• JSON/CSV-ready summary (optional)
• GitHub release tagging and PyPI publish automation

Installation

pip install seq-miner

Or clone from source:

git clone https://github.com/your-org/seq-miner.git
cd seq-miner
pip install .

Usage

Extract reads from BAM

seq-miner -i reads.bam -o filtered.bam -f bam -r read_ids.txt --min-qscore 10 --min-length 200

Filter FASTQ reads in parallel

seq-miner -i reads.fastq -o filtered.fastq -f fastq --min-qscore 15 --min-length 1000 --threads 4

Show version

seq-miner --version

Command-line Options

Option	Description
-i, --input	Input BAM or FASTQ file
-o, --output	Output file for passed reads
-f, --format	File format: bam or fastq
-r, --read-ids	Optional file with read IDs (one per line)
--min-qscore	Minimum mean Q-score (default: 0.0)
--min-length	Minimum read length (default: 0)
--threads	Number of CPU threads (only used for FASTQ)
--verbose	Enable verbose logging
--version	Print the current version

Output Summary

When finished, you'll see:

Summary:
Passed reads     : 12345
Low-quality reads : 54
Short reads      : 91

Optionally, you can pipe this to JSON or CSV (coming soon).

Auto Version + Release

• Version is stored in seqminer/__version__.py
• Tagged automatically with GitHub Actions on push to main
• Published to PyPI on GitHub release

License

MIT License © Theerayut
See LICENSE for full text.

Contact

For issues, please open an issue on GitHub.