Metadata-Version: 1.1
Name: genprimers
Version: 0.0.1
Summary: A software to design PCR primers for a a subset of  sequences which belong to a greater set
Home-page: https://bitbucket.org/lbmg/genprimers
Author: Diego Diaz Dominguez
Author-email: ddiaz@dim.uchile.cl
License: BSD
Description: 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
        
Keywords: PCR primers designer
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
