getMultiPrimerSet 1.0.0

A package for generating multiplex PCR primer sets

This program designs PCR primers for a multiplex of given target regions of a DNA sequence in a FASTA file.

The script takes several arguments:

Parameter	Description
region_file (required)	The path to the primer design region file. This file should have three columns: name, start position, and end position (1-based). It can be in either tsv or xlxs format.
input_file (required)	The path to the input FASTA file.
target_tm	The desired melting temperature (Tm) for the primers. Default is 60.
primer_len	The desired length of the primers. Default is 20.
product_size_min	The desired min size for the PCR product. Default is 400.
product_size_max	The desired max size for the PCR product. Default is 800.
ret	The maximum number of primer pairs to return. Default is 100.
Q5	A boolean indicating whether to use NEB Q5 hotstart polymerase settings for primer3. Default is True.
background	The path to the mispriming library FASTA file. Default is an empty string.
output	The name of the output file. Default is 'MultiPlexPrimerSet'.
eval	The maximum number of primer sets to evaluate. Default is 10000.

The main function of the script is 'design_primers', which takes the input FASTA file, start and end positions of a target region, and the arguments specified using argparse, and returns the best primer set for that region as a list of dictionaries containing information about the primer pairs.

The 'design_primers' function performs the following steps:

• Parses the input FASTA file and extracts the target region sequence.
• Sets up the primer3 input parameters based on the specified arguments.
• Runs primer3 to design the primers.
• Extracts information about the primer pairs.
• Determines the best set of multiplex primers.

Installation

pip install getMultiPrimerSet

Example usage

getMultiPrimerSet --region_file "./example/primer_regions.tsv" --input_file "./example/ref.fasta" --target_tm 65 --primer_len 20 --product_size_min 400 --product_size_max 800 --ret 100 --eval 1000 --Q5 --background "" --output "example"