Metadata-Version: 1.1
Name: vaxrank
Version: 0.4.5
Summary: Mutant peptide ranking for personalized cancer vaccines
Home-page: https://github.com/hammerlab/vaxrank
Author: Alex Rubinsteyn
Author-email: alex.rubinsteyn@gmail.com
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: |Build Status| |Coverage Status|
        
        vaxrank
        =======
        
        Selection of mutated protein fragments for therapeutic personalized
        cancer vaccines.
        
        Usage
        -----
        
        .. code:: sh
        
        
            vaxrank \
                --vcf test/data/b16.f10/b16.vcf \
                --bam test/data/b16.f10/b16.combined.bam \
                --vaccine-peptide-length 25 \
                --mhc-predictor netmhc \
                --mhc-alleles H2-Kb,H2-Db \
                --padding-around-mutation 5 \
                --output-ascii-report vaccine-peptides.txt \
                --output-pdf-report vaccine-peptides.pdf \
                --output-html-report vaccine-peptides.html
        
        Installation
        ------------
        
        Vaxrank can be installed using
        `pip <https://packaging.python.org/installing/#use-pip-for-installing>`__:
        
        ::
        
            pip install vaxrank
        
        Note: to generate PDF reports, you first need to install
        `wkhtmltopdf <http://wkhtmltopdf.org/>`__, which you can do (on OS X)
        like so:
        
        ::
        
            brew install Caskroom/cask/wkhtmltopdf
        
        Vaxrank uses `PyEnsembl <https://github.com/hammerlab/pyensembl>`__ for
        accessing information about the reference genome. You must install an
        Ensembl release corresponding to the reference genome associated with
        the mutations provided to Vaxrank.
        
        The latest release for GRCh38 is Ensembl 87:
        
        ::
        
            pyensembl install --release 87 --species human
        
        The last release for GRCh37 is Ensembl 75:
        
        ::
        
            pyensembl install --release 75 --species human
        
        If your variants were called from alignments against hg19 then you can
        still use GRCh37 but should ignore mitochondrial variants.
        
        Development
        ===========
        
        To install Vaxrank for local development, you may do the below:
        
        ::
        
            git clone git@github.com:hammerlab/vaxrank.git
            conda create -q -n vaxrank-dev-env python=3.5.2 numpy scipy nose pandas pylint
            source activate vaxrank-dev-env
            pip install -r requirements.txt
            pip install .
            pyensembl install --release 85 --species human
            pyensembl install --release 85 --species mouse
        
        You should run the linter and the test suite as you work on Vaxrank (and
        these will be run automatically by our continuous integration server up
        on a PR being made).
        
        ::
        
            ./lint.sh
            nosetests test
        
        The first run of the tests may take a while (8 minutes on a 2016 Macbook
        Pro) to create the FM index of the proteome, but subsequent tests should
        take only a few seconds.
        
        .. |Build Status| image:: https://travis-ci.org/hammerlab/vaxrank.svg?branch=master
           :target: https://travis-ci.org/hammerlab/vaxrank
        .. |Coverage Status| image:: https://coveralls.io/repos/github/hammerlab/vaxrank/badge.svg?branch=master
           :target: https://coveralls.io/github/hammerlab/vaxrank?branch=master
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
