Primertool
The premise of this package is to generate primers for PCR/Sanger sequencing for either:
a specific variant (hgvs variant nomenclature), either the whole exon or if not in an exon for the genomic position
an exon (transcript number and exon )
all exons of a transcript (transcript number)
around a genomic position (chromosome and start/stop position)
This tool allows for primers based the human reference genome version hg19 or hg38.
This project can be used in three ways. The core functionality of this tool is contained in the primertool python package inside this project and can be used via the command line (usage examples below). The streamlit app also contained in this project is simply a wrapper around the core functionality of the primertool package to make the tool accessible to non-programmers. The streamlit app can be run locally or deployed to a server. For proper deployment and management a Dockerfile is also provided.
Usage options:
python package
streamlit app (recommended for development)
docker container (recommended for deployment)
Overview
For a detailed overview of how the tool generates primers, please refer to the information page. The software documentation is available in the modules page. For instructions on how to set up the tool, please refer to the setup page.
Installation
Using the python package requires Python 3.8+. All required packages are listed in the requirements file.
Local installation is possible by running
conda env create -f environment.yml
in the main directory (requires conda and pip installed).
You will also need gcc installed on your system, so check if you already have it by running
gcc --version
If you don’t have gcc installed, you can install it by running
sudo apt update
sudo apt install build-essential
For the streamlit app and docker container, the setup instructions are provided in the setup guide. When running the tool behind a firewall and it is not possible to access the hg38 genome database (or a local version is wanted for other reasons), it is possible to run a local instance of said database. To create such a local MySQL instance follow the steps described here: MySQL setup guide
Basic usage examples
Generating primers for a mutation using VariantPrimerGenerator:
from primertool import primertool as pt
df = pt.VariantPrimerGenerator('NM_003165.6:c.1702G>A', 'hg38', kuerzel='SM').ordertable
Generating primer for a single exon using ExonPrimerGenerator:
from primertool import primertool as pt
df = pt.ExonPrimerGenerator('NM_000451', 6, 'hg38', kuerzel='SM').ordertable
Generating primers for every exon in a gene using GenePrimerGenerator:
from primertool import primertool as pt
df = pt.GenePrimerGenerator('NM_000451', 'hg38', kuerzel='SM').ordertable
Generating primer for a genomic position using GenomicPositionPrimerGenerator:
from primertool import primertool as pt
df = pt.GenomicPositionPrimerGenerator('chr12', 121814175, 121814175, 'hg38', kuerzel='SM').ordertable
Contents