semvec/pypi-packages huggingface dataset:
genprimers 0.0.1
A software to design PCR primers for a a subset of  sequences which belong to a greater set
License: BSD
Keywords: PCR primers designer

Genprimers
==========

Genprimers is a software aimed to produce PCR primers. Unlike other
primers programs, such as primer3, it is focused on generating specific
primers for a set the sequences (defined as targets) which are a subset
of a greater set of sequences (defined as the universe). This is very
useful for example when we have 16S amplicon experiments from ambiental
samples, which have a lot of different miroorganisms, and we are
interested in detecting spefific *phylums* or *clades*. Genprimers is
also useful when we have to amplify a specific biomarker of a subset of
individuals belonging to a greater set of closely- related
microorganism.

Prerequisites
=============

-  Bowtie 1
-  Python 2.7
-  Cython

For the moment, Bowtie 1 is necessary to run genprimers. In the future,
this won't be necessary.

How to install
==============

Automatic install
-----------------

Genprimers is available in the Python pip repository

::

    $ pip install genprimers

Manual install
--------------

Clone the git repository in your local machine

::

    $ git clone git@bitbucket.org:lbmg/genprimers.git

Enter to the cloned repository

::

    $ cd genprimers

Install using the python install framework

::

    $ python setup.py install

Examples
========

Generating the index for the universe
-------------------------------------

In order to run genprimers, the input FASTA file must be indexed with
Bowtie (for the moment)

::

    $ bowtie-build universe.fna universe.fna

Running genprimers
------------------

Assuming we already have the FASTA file of the universe indexed with
bowtie and a one-column file containing the IDs of a subset of sequences
of the universe we want to amplify (targets\_ids.txt in this example),
run genprimers is as easy as:

::

    $ genprimers primers universe.fna targets_ids.txt output_folder

The list of targets IDs can be passed through the standard input

::

    $ cat targets_ids.txt | genprimers primers universe.fna output_folder

Listing all the sequences in the Universe
-----------------------------------------

In order to run Genprimers you need the IDs of the targets in the FASTA
file of the universe, but often we don't know those identifier. To list
the IDs in the universe, and their respectives descriptions, we can use
the list command from genprimers.

::

    $ genprimers list unvierse.fna

We can filter the output list to report only those sequences belonging
to some class and then use that list to design primers. In the example
below we list all the sequences that fit the *Gluconobacter genus*
description and produce new primers for this subset:

::

    $genprimers list universe.fna | grep Gluconobacter | cut -f1 | genprimers primer universe.fna output_prefix