Package: primkit
primkit - Primer ToolkitIntroductionprimkitis a comprehensive tool designed to facilitate the primer design process for various molecular biology applications. It assists researchers with the creation, analysis, and preprocessing of primer results, optimizing both convenience and efficiency.FeaturesAutomated Primer Design: Quickly generate primers suited to your specific requirements.Compatibility Check: Verify the compatibility of your primers with target sequences.Result Preprocessing: Easily format and preprocess your primer design outcomes.User-Friendly: An intuitive tool for both experienced and novice users in bioinformatics.InstallationFrom PyPIYou can install the released version ofprimkitfrom PyPI with a simple pip command:pipinstallprimkitMake sure you have Python 3.6 or later installed.Using a MirrorFor users in China, or in case the PyPI is slow or restricted in your location, you may opt to use a Chinese mirror. Here are examples using Aliyun and Tencent Cloud mirrors:Using Aliyun:pipinstallprimkit-ihttps://mirrors.aliyun.com/pypi/simple/Using Tencent Cloud:pipinstallprimkit-ihttps://mirrors.cloud.tencent.com/pypi/simpleFrom GitHub (Using pip)To install the latest version directly from GitHub using pip:pipinstallgit+https://github.com/Enthusiasm23/primkit.gitFrom Source (Using git clone and setup.py)If you prefer to install from source for a development environment, you can clone the repository and usesetup.py:gitclonehttps://github.com/Enthusiasm23/primkit.gitcdprimkit
pythonsetup.pyinstallNote: Installing directly from GitHub is recommended for developers or if you need features that have not yet been released to PyPI.UsageAfter installingprimkit, you can use it to design primers with your specific requirements. Here is a basic example of how to useprimkit:importprimkit# Define your primer design parametersprimer_data={'DB':'hg19.fa',# Reference database'SnpFilter':'yes',# SNP filtering option'PrimerMinSize':'17',# Minimum size of the primer'PrimerOptSize':'22',# Optimal size of the primer'PrimerMaxSize':'25',# Maximum size of the primer'PrimerMinTm':'58',# Minimum melting temperature of the primer'PrimerOptTm':'60',# Optimal melting temperature of the primer'PrimerMaxTm':'62',# Maximum melting temperature of the primer'ProdMinSize':'80',# Minimum size of the product'ProdMaxSize':'120',# Maximum size of the product'DimerScore':'5',# Maximum acceptable dimer score'HairpinScore':'5',# Maximum acceptable hairpin score'Tm':'47',# Annealing temperature'SpecMinSize':'0',# Minimum size for specificity check'SpecMaxSize':'500',# Maximum size for specificity check'BedInput':'chr7\t55249070\t55249073\nchr22\t42538507\t42538510\n...'# Target regions in BED format}# Call the design_primers function with the primer dataprimer_result=primkit.design_primers(primer_data)# The 'primer_result' variable will contain the results of the primer designt primkitFor comprehensive guides and usage examples, check thedocumentation.ContributingContributions to primkit are welcome! Feel free to submit pull requests or open issues to propose enhancements or add new features.Acknowledgments and Disclaimerprimkitserves as a convenient interface for primer design, building upon the robust primer design capabilities ofMFEprimer3. We extend our sincere gratitude to the original authors of MFEprimer-3.0 for their significant contributions to the scientific community. You can find the original MFEprimer-3.0 tool and source code on theirGitHub repository.Whileprimkitaims to simplify the primer design process, users who intend to apply this for commercial purposes should do so with caution. We do not guarantee the correctness of the primer design results generated byprimkit. For rigorous and commercial-grade applications, we recommend using theoriginal MFEprimer-3.0 web interfacedirectly.Licenseprimkitis released under the MIT License. See theLICENSEfile for details.ContactIf you have any questions or feedback, reach out to us atlbfeng23@gmail.com.Enjoy using primkit, and may your primer design be effortless and precise!