Metadata-Version: 1.1
Name: topiary
Version: 0.0.5
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: Topiary
        =======
        
        Predict mutation-derived cancer T-cell epitopes from (1) somatic
        variants (2) tumor RNA expression data, and (3) patient HLA type.
        
        Example
        -------
        
        .. code:: sh
        
            ./topiary \
              --vcf somatic.vcf \
              --mhc-pan \
              --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-file genes.fpkm_tracking \
              --rna-min-gene-expression 4.0 \
              --rna-transcript-fpkm-file isoforms.fpkm_tracking \
              --rna-min-transcript-expression 1.5 \
              --output-csv epitopes.csv \
              --output-html epitopes.html
        
        Commandline Arguments
        ---------------------
        
        Genomic Variants
        ~~~~~~~~~~~~~~~~
        
        You must specify at least one variant input file:
        
        -  ``--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
        
        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-file RNA_GENE_FPKM_FILE``: Cufflinks FPKM tracking
           file containing gene expression estimates.
        -  ``--rna-min-gene-expression RNA_MIN_GENE_EXPRESSION``: Minimum FPKM
           for genes
        -  ``--rna-remap-novel-genes-onto-ensembl``: If a novel gene is fully
           contained within a known Ensembl gene, remap its FPKM expression
           value on the Ensembl gene ID.
        -  ``--rna-transcript-fpkm-file RNA_TRANSCRIPT_FPKM_FILE``: Cufflinks
           FPKM tracking file containing transcript expression estimates.
        -  ``--rna-min-transcript-expression RNA_MIN_TRANSCRIPT_EXPRESSION``:
           Minimum FPKM for transcripts
        
        Choose an MHC Binding Predictor
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        You *must* choose an MHC binding predictor using one of the following
        flags:
        
        -  ``--mhc-pan``: Local NetMHCpan
        -  ``--mhc-cons``: Local NetMHCcons
        -  ``--mhc-random``: Random IC50 values
        -  ``--mhc-smm``: Local SMM
        -  ``--mhc-smm-pmbec``: Local SMM-PMBEC
        -  ``--mhc-pan-iedb``: NetMHCpan via the IEDB web API
        -  ``--mhc-cons-iedb``: NetMHCcons via the IEDB web API
        -  ``--mhc-smm-iedb``: SMM via the IEDB web API
        -  ``--mhc-smm-pmbec-iedb``: 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
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``--keep-wildtype-epitopes``: Topiary will normally discard predicted
           epitopes which don't overlap a mutated region of a protein. Use this
           flag to keep all predicted epitopes you must this
        -  ``--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 combined with
           ``--keep-wildtype-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.
        
        
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
