Metadata-Version: 1.1
Name: topiary
Version: 0.0.16
Summary: Predict cancer epitopes from cancer sequence data
Home-page: https://github.com/hammerlab/topiary
Author: Alex Rubinsteyn, Tavi Nathanson
Author-email: alex {dot} rubinsteyn {at} gmail {dot} com
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: `|Build Status| <https://travis-ci.org/hammerlab/topiary>`_ `|Coverage
        Status| <https://coveralls.io/github/hammerlab/topiary?branch=master>`_
        `|DOI| <https://zenodo.org/badge/latestdoi/18834/hammerlab/topiary>`_
        
        Topiary
        =======
        
        Predict mutation-derived cancer T-cell epitopes from (1) somatic
        variants (2) tumor RNA expression data, and (3) patient HLA type.
        
        Example
        -------
        
        ::
        
            ./topiary \
              --vcf somatic.vcf \
              --mhc-predictor netmhcpan \
              --mhc-alleles HLA-A*02:01,HLA-B*07:02 \
              --ic50-cutoff 500 \
              --percentile-cutoff 2.0 \
              --mhc-epitope-lengths 8-11 \
              --rna-gene-fpkm-tracking-file genes.fpkm_tracking \
              --rna-min-gene-expression 4.0 \
              --rna-transcript-fpkm-tracking-file isoforms.fpkm_tracking \
              --rna-min-transcript-expression 1.5 \
              --output-csv epitopes.csv \
              --output-html epitopes.html
        
        Installation
        ------------
        
        You can install Topiary and all of the libraries it depends on by
        running: ``pip install topiary``
        
        You'll need to download the reference genome sequences and annotations
        for a recent Ensembl release (e.g. 81) by running:
        
        ::
        
            pyensembl install --release 81 --species human
        
        If you want to work with variants which were aligned against the older
        reference GRCh37, you will need to also download its annotation data,
        which is contained in Ensembl release 75:
        
        ::
        
            pyensembl install --release 75 --species human
        
        Commandline Arguments
        ---------------------
        
        Genomic Variants
        ~~~~~~~~~~~~~~~~
        
        Specify some variants by giving at least one of the following options.
        They can be used in combination and repeated.
        
        -  ``--vcf VCF_FILENAME``: Load a
           `VCF <http://www.1000genomes.org/wiki/analysis/variant%20call%20format/vcf-variant-call-format-version-41>`_
           file
        -  ``--maf MAF_FILENAME``: Load a TCGA
           `MAF <https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification>`_
           file
        -  ``--variant CHR POS REF ALT : Specify an individual variant (requires --ensembl-version)``
        
        Output Format
        ~~~~~~~~~~~~~
        
        -  ``--output-csv OUTPUT_CSV_FILENAME``: Path to an output CSV file
        -  ``--output-html OUTPUT_HTML_FILENAME``: Path to an output HTML file
        
        RNA Expression Filtering
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        Optional flags to use Cufflinks expression estimates for dropping
        epitopes arising from genes or transcripts that are not highly
        expressed.
        
        -  ``--rna-gene-fpkm-tracking-file RNA_GENE_FPKM_TRACKING_FILE``:
           Cufflinks FPKM tracking file containing gene expression estimates.
        -  ``--rna-min-gene-expression RNA_MIN_GENE_EXPRESSION``: Minimum FPKM
           for genes
        -  ``--rna-transcript-fpkm-tracking-file RNA_TRANSCRIPT_FPKM_TRACKING_FILE``:
           Cufflinks FPKM tracking file containing transcript expression
           estimates.
        -  ``--rna-min-transcript-expression RNA_MIN_TRANSCRIPT_EXPRESSION``:
           Minimum FPKM for transcripts
        -  ``--rna-transcript-fpkm-gtf-file RNA_TRANSCRIPT_FPKM_GTF_FILE``:
           StringTie GTF file file containing transcript expression estimates.
        
        Choose an MHC Binding Predictor
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        You *must* choose an MHC binding predictor using one of the following
        values for the ``--mhc-predictor`` flag:
        
        -  ``netmhc``: Local
           `NetMHC <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC>`_
           predictor (Topiary will attempt to automatically detect whether
           NetMHC 3.x or 4.0 is available)
        -  ``netmhcpan``: Local
           `NetMHCpan <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan>`_
           predictor
        -  ``netmhciipan``: Local
           `NetMHCIIpan <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan>`_
           predictor
        -  ``netmhccons``: Local
           `NetMHCcons <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCcons>`_
        -  ``random``: Random IC50 values
        -  ``smm``: Local `SMM <http://www.mhc-pathway.net/smm>`_ predictor
        -  ``smm-pmbec``: Local
           `SMM-PMBEC <http://www.mhc-pathway.net/smmpmbec>`_ predictor
        -  ``netmhcpan-iedb``: Use NetMHCpan via the IEDB web API
        -  ``netmhccons-iedb``: Use NetMHCcons via the IEDB web API
        -  ``smm-iedb``: Use SMM via the IEDB web API
        -  ``smm-pmbec-iedb``: Use SMM-PMBEC via the IEDB web API
        
        MHC Alleles
        ~~~~~~~~~~~
        
        You must specify the alleles to perform binding prediction for using one
        of the following flags:
        
        -  ``--mhc-alleles-file MHC_ALLELES_FILE``: Text file containing one
           allele name per line
        -  ``--mhc-alleles MHC_ALLELES``: Comma separated list of allele names,
           e.g. "HLA-A02:01,HLA-B07:02"
        
        Peptide Length
        ~~~~~~~~~~~~~~
        
        -  ``--mhc-epitope-lengths MHC_EPITOPE_LENGTHS``: comma separated list
           of integers specifying which peptide lengths to use for MHC binding
           prediction
        
        Binding Prediction Filtering
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``--only-novel-epitopes``: Topiary will normally keep all predicted
           epitopes, even those which occur in a given self-ligandome or don't
           overlap a mutated region of a protein. Use this flag to drop any
           epitopes which don't contain mutations or that occur elsewhere in the
           self-ligandome.
        -  ``--ic50-cutoff IC50_CUTOFF``: Drop peptides with predicted IC50 nM
           greater than this value (typical value is 500.0)
        -  ``--percentile-cutoff PERCENTILE_CUTOFF``: Drop peptides with
           percentile rank of their predicted IC50 (among predictions for a
           particular allele) fall below this threshold (lower values are
           stricter filters, typical value is 2.0)
        
        Misc
        ~~~~
        
        -  ``--padding-around-mutation PADDING_AROUND_MUTATION``: Include more
           unmutated residues around the mutation (useful when not using
           ``--only-novel-epitopes``)
        -  ``--self-filter-directory SELF_FILTER_DIRECTORY``: Directory of files
           named by MHC allele containing a self peptide ligandome (peptides
           which should be excluded from results)
        -  ``--skip-variant-errors``: If a particular mutation causes an
           exception to be raised during annotation, you can skip it using this
           flag.
        
        .. |Build
        Status| image:: https://travis-ci.org/hammerlab/topiary.svg?branch=master
        .. |Coverage
        Status| image:: https://coveralls.io/repos/hammerlab/topiary/badge.svg?branch=master&service=github
        .. |DOI| image:: https://zenodo.org/badge/18834/hammerlab/topiary.svg
        
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
