Some functions to count the expected amplifications for genomic regions given a set of primer binding locations for a multiple displacement amplification reaction.
Some python functions to count the expected amplifications for genomic regions given a set of primer binding locations for a multiple displacement amplification reaction. See ampCountR for more details.
The easy way to install is to just do:
pip install ampcountpy
To install the development version from github, clone the repository to a local directory using something like:
git clone https://github.com/sherrillmix/ampcountpy.git
and run setup.py from the resulting directory (the –user installs it locally and doesn’t require root access):
cd ampcountpy python setup.py install --user python setup.py test
The module can be called directly using something like:
python -m ampcountpy -f forward.txt -r reverse.txt
ampcountpy -f forward.txt -r reverse.txt
where forward.txt is a text file containing position of primer landing sites on the forward strand and reverse.txt is primer landing sites on the reverse strand. By default, amplification predictions are output to out.csv. The full details on options and arguments is available with:
Using function in python
The main function is predictAmplifications which can be used like:
from ampcountpy import predictAmplifications forwards=[1,2,3] reverses=[5,6,7] predictions=predictAmplifications(forwards,reverses)
where forwards are the 5’-most base of primer landing sites on the forward strand and reverses are the 3’-most base of primers landing on the reverse strand.
- Count non-overlapping primers correctly
- Fix header
- Fix changelog formatting
- Pip install instructions
- Initial public release