PrimerBLAST Parser

Parse Primer-BLAST or primerblaster text output and export primer pairs as FASTA.

The main workflow groups Primer-BLAST sections by gene, filters by specificity, and writes forward and reverse primer sequences for downstream tools.

Installation

git clone <remote-url>
cd primerblaster-parser
python3 -m venv .venv
source .venv/bin/activate
python -m pip install -e .

Usage

primerblaster-parser \
  --input examples/primerblast.txt \
  --output primers.fa \
  hits-per-gene --specific 1

Run the module directly:

python -m primerblaster_parser.primerblaster_parser \
  --input examples/primerblast.txt \
  --output primers.fa \
  hits-per-gene --specific 1

Useful options for hits-per-gene:

• --specific N or --specific MIN-MAX: keep jobs with products in range
• --not-specific: exclude jobs with exactly one product
• --mismatch: keep jobs with template mismatches
• --full-match first|all: require perfect template matches
• --pick-best: keep the best-scoring primer header per gene
• --group-by-annotation --annotation annotations.tsv: group output by annotation

Development

python -m py_compile primerblaster_parser/primerblaster_parser.py

License

MIT License. See LICENSE.