mascpcr

mascpcr is a toolkit and configurable pipeline for generating multiplex allele-specific colony (MASC) PCR primer sets.

Features:

• "Minimal input" pipeline -- requires 2 genbank files and target region indices to produce standard MASC PCR primer sets
• Module-based and command line interfaces
• Detailed reporting and order-ready .xlsx output
• Low level toolkit for more sophisticated MASC PCR-related design tasks

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Installation

Python library dependencies

1. Make sure you have setuptools installed (pip install setuptools).

2. Install the necessary dependencies in the following order:

   cython
   biopython bitarray numpy openpyxl primer3-py six
   https://github.com/Wyss/libnano
   https://github.com/Wyss/mauve-py
   

3. (optional) Run setup.py install to install the package on your PYTHONPATH.

Use of a virtualenv is encouraged. For more configurable installation options, see the docs.

Usage

The simplest way to use mascpcr is via the command line interface:

$ mascpcrcli recoded_genome.gb reference_genome.gb 1202000 1252000
     (1)            (2)                (3)           (4)     (5)

1. CLI script installed in your PATH
2. Recoded / modified genome genbank file
3. Reference genome genbank file
4. MASC primer design start index
5. MASC primer design end index (inclusive)

Of course, mascpcr can also be imported and used as a Python module. See examples/ for some example use cases, and docs/ for more information.

Future plans

mascpcr functions well for our current needs, so we have no immediate plans for further development. That being said, we are happy to help you expand / adapt the code base for your specific project needs.

License

Copyright (C) 2014. Copyright (c) 2014 Wyss Institute at Harvard University

Ben Pruitt & Nick Conway

See LICENSE for full GPLv2 license.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.