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        "author": "Diego Diaz Dominguez",
        "author_email": "ddiaz@dim.uchile.cl",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "Genprimers\n==========\n\nGenprimers is a software aimed to produce PCR primers. Unlike other\nprimers programs, such as primer3, it is focused on generating specific\nprimers for a set the sequences (defined as targets) which are a subset\nof a greater set of sequences (defined as the universe). This is very\nuseful for example when we have 16S amplicon experiments from ambiental\nsamples, which have a lot of different miroorganisms, and we are\ninterested in detecting spefific *phylums* or *clades*. Genprimers is\nalso useful when we have to amplify a specific biomarker of a subset of\nindividuals belonging to a greater set of closely- related\nmicroorganism.\n\nPrerequisites\n=============\n\n-  Bowtie 1\n-  Python 2.7\n-  Cython\n\nFor the moment, Bowtie 1 is necessary to run genprimers. In the future,\nthis won't be necessary.\n\nHow to install\n==============\n\nAutomatic install\n-----------------\n\nGenprimers is available in the Python pip repository\n\n::\n\n    $ pip install genprimers\n\nManual install\n--------------\n\nClone the git repository in your local machine\n\n::\n\n    $ git clone git@bitbucket.org:lbmg/genprimers.git\n\nEnter to the cloned repository\n\n::\n\n    $ cd genprimers\n\nInstall using the python install framework\n\n::\n\n    $ python setup.py install\n\nExamples\n========\n\nGenerating the index for the universe\n-------------------------------------\n\nIn order to run genprimers, the input FASTA file must be indexed with\nBowtie (for the moment)\n\n::\n\n    $ bowtie-build universe.fna universe.fna\n\nRunning genprimers\n------------------\n\nAssuming we already have the FASTA file of the universe indexed with\nbowtie and a one-column file containing the IDs of a subset of sequences\nof the universe we want to amplify (targets\\_ids.txt in this example),\nrun genprimers is as easy as:\n\n::\n\n    $ genprimers primers universe.fna targets_ids.txt output_folder\n\nThe list of targets IDs can be passed through the standard input\n\n::\n\n    $ cat targets_ids.txt | genprimers primers universe.fna output_folder\n\nListing all the sequences in the Universe\n-----------------------------------------\n\nIn order to run Genprimers you need the IDs of the targets in the FASTA\nfile of the universe, but often we don't know those identifier. To list\nthe IDs in the universe, and their respectives descriptions, we can use\nthe list command from genprimers.\n\n::\n\n    $ genprimers list unvierse.fna\n\nWe can filter the output list to report only those sequences belonging\nto some class and then use that list to design primers. In the example\nbelow we list all the sequences that fit the *Gluconobacter genus*\ndescription and produce new primers for this subset:\n\n::\n\n    $genprimers list universe.fna | grep Gluconobacter | cut -f1 | genprimers primer universe.fna output_prefix",
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        "keywords": "PCR primers designer",
        "license": "BSD",
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        "name": "genprimers",
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        "summary": "A software to design PCR primers for a a subset of  sequences which belong to a greater set",
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