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Some functions to count the expected amplifications for genomic regions given a set of primer binding locations for a multiple displacement amplification reaction.

Project description

Travis CI Codecov PyPi version

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.

Installation

Easy install

The easy way to install is to just do:

pip install ampcountpy

Github

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

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

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
ampcountpy-0.2.0.tar.gz (6.2 kB) Copy SHA256 hash SHA256 Source None Dec 8, 2015

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