Installation

pip install ampcountpy

git clone https://github.com/sherrillmix/ampcountpy.git

cd ampcountpy
python setup.py install --user
python setup.py test

Run directly

The module can be called directly using something like:

python -m ampcountpy -f forward.txt -r reverse.txt

or:

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:

ampcountpy --help

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.

Changelog

0.2.0 (2015-12-08)

• Count non-overlapping primers correctly

0.1.3 (2015-11-02)

• Fix header

0.1.2 (2015-11-02)

• Fix changelog formatting

0.1.1 (2015-11-02)

• Pip install instructions

0.1.0 (2015-11-02)

• Initial public release