primerlab stats

CLI reference for the primerlab stats command

Analyze sequence statistics before primer design.

New in v0.1.6

Synopsis

primerlab stats <sequence> [options]

Arguments

Argument	Required	Description
sequence	Yes	Path to FASTA file or raw sequence

Options

Option	Short	Description
--json	-j	Output as JSON

Output

The stats command displays:

• Length — Sequence length in base pairs
• GC Content — GC percentage and count
• AT Content — AT percentage and count
• N Count — Number of masked (N) bases
• IUPAC Codes — Detected ambiguous codes
• RNA Detection — Whether sequence contains uracil (U)

Examples

Basic Usage

primerlab stats input.fasta

Output:

📊 Sequence Statistics: GAPDH
=============================================
  Length:      3,605 bp
  GC Content:  50.98% (1,838 bp)
  AT Content:  49.02% (1,767 bp)
=============================================
✅ Ready for primer design

JSON Output

primerlab stats input.fasta --json

Output:

{
  "name": "GAPDH",
  "length": 3605,
  "gc_percent": 50.98,
  "gc_count": 1838,
  "at_count": 1767,
  "n_count": 0,
  "iupac_codes": [],
  "iupac_count": 0,
  "has_uracil": false,
  "valid_for_design": true
}

With Masked Regions

primerlab stats masked_sequence.fasta

Output:

📊 Sequence Statistics: TEST_MASKED
=============================================
  Length:      1,178 bp
  GC Content:  53.99% (636 bp)
  AT Content:  41.26% (486 bp)
  N (masked):  56 bp (4.75%)
=============================================
✅ Ready for primer design

With IUPAC Codes

primerlab stats sequence_with_iupac.fasta

Output:

📊 Sequence Statistics: TEST_IUPAC
=============================================
  Length:      500 bp
  GC Content:  48.20% (241 bp)
  AT Content:  50.60% (253 bp)
  ⚠️  IUPAC codes: ['R', 'Y'] (6 bp)
      → Will be converted to N during design
=============================================
✅ Ready for primer design

Use Cases

1. Pre-flight check — Verify sequence before design
2. Pipeline scripting — Use --json for automated workflows
3. Troubleshooting — Identify problematic sequences