primerlab species-check

CLI reference for the primerlab species-check command

Check primer specificity across multiple species templates.

Synopsis

primerlab species-check --primers FILE --target FILE [OPTIONS]

Description

The species-check command analyzes primer binding across target and off-target species to ensure specificity. It calculates binding scores, identifies cross-reactivity risks, and generates detailed reports.

Arguments

Argument	Required	Description
--primers, -p	Yes	Path to primers JSON file
--target, -t	Yes	Path to target species FASTA
--offtargets	No	Comma-separated off-target FASTA files
--output, -o	No	Output directory (default: species_check_output)
--format	No	Report format: markdown, json, excel, html (default: markdown)
--primers-dir	No	Directory with multiple primer JSON files (batch mode)
--parallel	No	Number of threads for batch processing (default: 4)
--no-cache	No	Disable SQLite caching

Examples

Basic Usage

primerlab species-check \
  --primers primers.json \
  --target human_template.fasta

With Off-targets

primerlab species-check \
  --primers primers.json \
  --target human.fasta \
  --offtargets mouse.fasta,rat.fasta \
  --output results/

Batch Mode

primerlab species-check \
  --primers-dir primers_directory/ \
  --target human.fasta \
  --parallel 4 \
  --output batch_results/

HTML Report

primerlab species-check \
  --primers primers.json \
  --target human.fasta \
  --format html

Input Format

primers.json

[
  {"name": "Gene1", "forward": "ATGCGATCGATCGATCGATCG", "reverse": "CGATCGATCGATCGATCGCAT"},
  {"name": "Gene2", "forward": "GCTAGCTAGCTAGCTAGCTAG", "reverse": "TAGCTAGCTAGCTAGCTAGCT"}
]

FASTA Files

>SpeciesName
ATGCGATCGATCGATCGATCG...

Output

Console Output

🧬 Species Specificity Check (v0.4.3)
==================================================
📂 Loading primers: primers.json
🎯 Target: Human (350 bp)
🔬 Off-targets: Mouse, Rat

⏳ Analyzing 2 primer pairs...

==================================================
📊 Specificity Results:
   Gene1: Score 95.0 (Grade A) ✅ SPECIFIC
   Gene2: Score 87.5 (Grade B) ✅ SPECIFIC

🎯 Overall: 91.3 (Grade A)
   Specific: 2/2 (100%)

📁 Report saved to: species_check_output/species_analysis.md

Report Files

• species_analysis.json - Full JSON data
• species_analysis.md - Markdown report
• species_analysis.html - HTML report
• species_analysis.xlsx - Excel workbook

Scoring

Score	Grade	Meaning
≥90	A	Excellent specificity
80-89	B	Good specificity
70-79	C	Acceptable
60-69	D	Poor - review recommended
<60	F	Fail - redesign required

See Also

• Species Specificity Feature
• Species Check Tutorial
• Batch Processing