primerD 0.1.1

A Python package for designing PCR primers

primerD

primerD: a Python package for designing and generating primers from DNA sequences. It helps molecular biologists and bioinformatics researchers quickly obtain primer candidates for PCR and gene amplification.

Features

• Generate forward and reverse primers from DNA sequences.
• Evaluate GC content and melting temperature (Tm) for each primer.
• Detect hairpins and homodimer formations.
• Interactive GUI for easy primer design.
• Save primer reports as CSV files and visualize results with plots.

Requirements

• Python >= 3.8
• pandas
• matplotlib
• primer3-py

Installation

pip  install primerD .

## Usage: 

After installing primerD, you can easily generate primers from a DNA sequence:

from primerD import generate_primers, GC_content, Tm
from Bio import SeqIO

# Option 1: Manual DNA input
sequence = input("Enter DNA sequence: ").upper()

# Option 2: Read from FASTA file (uncomment if needed)
# fasta_file = "example.fasta"
# sequence = ""
# for record in SeqIO.parse(fasta_file, "fasta"):
#     sequence += str(record.seq).upper()

# Set primer length
primer_length = 18

# Generate primers
primers = generate_primers(sequence, primer_length=primer_length)

# Display primers with GC% and Tm
print(f"\nGenerated {len(primers)} primers (showing first 5):\n")
for i, p in enumerate(primers[:5], start=1):
    gc = GC_content(p)
    tm = Tm(p)
    print(f"Primer {i}: {p} | GC%: {gc:.2f} | Tm: {tm:.2f}آ°C")


# Parameters
Parameter	Type	Description
sequence	str	DNA sequence from which primers will be generated. Must contain only A, T, C, and G.
primer_length	int, optional	The length of each primer. Default is 20.