seq-miner 1.1.0

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 fast, Python-based command-line tool to extract and filter sequence reads from BAM and FASTQ files by:

• Read ID (single or batch)
• Mean quality score
• Minimum read length

Built for researchers working in genomics, transcriptomics, and metagenomics.

Installation

Install via pip:

pip install seq-miner

Usage

seq-miner --input INPUT --output OUTPUT --format FORMAT [options]

Example 1: Filter FASTQ reads by Q-score and length

seq-miner -i sample.fastq -o filtered.fastq -f fastq --min_qscore 15 --min_length 100

Example 2: Extract specific read IDs from a BAM file

seq-miner -i reads.bam -o matched.bam -f bam -r read_ids.txt --min_qscore 10 --min_length 200

Options

Flag	Description
-i, --input	Input BAM or FASTQ file
-o, --output	Output file to write filtered/passed reads
-f, --format	File format: bam or fastq
-r, --read_ids	File containing read IDs (one per line, optional)
--min_qscore	Minimum average quality score per read (default: 0)
--min_length	Minimum length per read (default: 0)

Input Examples

FASTQ file (.fastq)

Supports gzipped or plain FASTQ format.

BAM file (.bam)

Requires pysam under the hood.

Read ID file (optional)

read00001
read00044
read20398

Output

• Filtered reads saved to the specified output file.
• CLI prints counts of:
  • Passed reads
  • Low-quality reads
  • Short reads

Dependencies

• Biopython
• pysam

Installable automatically via pip install seq-miner.

Publishing (for maintainers)

To publish:

python -m build
twine upload dist/*

Or use GitHub Actions (see .github/workflows/pypi-release.yml) for trusted publishing.

License

MIT License © Theerayut
See LICENSE for full text.

Contact

For issues, please open an issue on GitHub.