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        "author": "Alex Rubinsteyn, Tavi Nathanson",
        "author_email": "alex.rubinsteyn@gmail.com",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Topiary\n=======\n\nPredict mutation-derived cancer T-cell epitopes from (1) somatic\nvariants (2) tumor RNA expression data, and (3) patient HLA type.\n\nExample\n-------\n\n.. code:: sh\n\n    ./topiary \\\n      --vcf somatic.vcf \\\n      --mhc-predictor netmhcpan \\\n      --mhc-alleles HLA-A*02:01,HLA-B*07:02 \\\n      --ic50-cutoff 500 \\\n      --percentile-cutoff 2.0 \\\n      --mhc-epitope-lengths 8-11 \\\n      --rna-gene-fpkm-tracking-file genes.fpkm_tracking \\\n      --rna-min-gene-expression 4.0 \\\n      --rna-transcript-fpkm-tracking-file isoforms.fpkm_tracking \\\n      --rna-min-transcript-expression 1.5 \\\n      --output-csv epitopes.csv \\\n      --output-html epitopes.html\n\nInstallation\n------------\n\nYou can install Topiary and all of the libraries it depends on by\nrunning:\n\n::\n\n    pip install topiary\n\nYou'll need to download the reference genome sequences and annotations\nfor a recent Ensembl release (e.g. 81) by running:\n\n::\n\n    pyensembl install --release 81 --species human\n\nIf you want to work with variants which were aligned against the older\nreference GRCh37, you will need to also download its annotation data,\nwhich is contained in Ensembl release 75:\n\n::\n\n    pyensembl install --release 75 --species human\n\nCommandline Arguments\n---------------------\n\nGenomic Variants\n~~~~~~~~~~~~~~~~\n\nSpecify some variants by giving at least one of the following options.\nThey can be used in combination and repeated.\n\n-  ``--vcf VCF_FILENAME``: Load a\n   `VCF <http://www.1000genomes.org/wiki/analysis/variant%20call%20format/vcf-variant-call-format-version-41>`__\n   file\n-  ``--maf MAF_FILENAME``: Load a TCGA\n   `MAF <https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification>`__\n   file\n-  ``--variant CHR POS REF ALT : Specify an individual variant (requires --ensembl-version)``\n\nOutput Format\n~~~~~~~~~~~~~\n\n-  ``--output-csv OUTPUT_CSV_FILENAME``: Path to an output CSV file\n-  ``--output-html OUTPUT_HTML_FILENAME``: Path to an output HTML file\n\nRNA Expression Filtering\n~~~~~~~~~~~~~~~~~~~~~~~~\n\nOptional flags to use Cufflinks expression estimates for dropping\nepitopes arising from genes or transcripts that are not highly\nexpressed.\n\n-  ``--rna-gene-fpkm-tracking-file RNA_GENE_FPKM_TRACKING_FILE``:\n   Cufflinks FPKM tracking file containing gene expression estimates.\n-  ``--rna-min-gene-expression RNA_MIN_GENE_EXPRESSION``: Minimum FPKM\n   for genes\n-  ``--rna-transcript-fpkm-tracking-file RNA_TRANSCRIPT_FPKM_TRACKING_FILE``:\n   Cufflinks FPKM tracking file containing transcript expression\n   estimates.\n-  ``--rna-min-transcript-expression RNA_MIN_TRANSCRIPT_EXPRESSION``:\n   Minimum FPKM for transcripts\n-  ``--rna-transcript-fpkm-gtf-file RNA_TRANSCRIPT_FPKM_GTF_FILE``:\n   StringTie GTF file file containing transcript expression estimates.\n\nChoose an MHC Binding Predictor\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nYou *must* choose an MHC binding predictor using one of the following\nvalues for the ``--mhc-predictor`` flag:\n\n-  ``netmhc``: Local\n   `NetMHC <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC>`__\n   predictor (Topiary will attempt to automatically detect whether\n   NetMHC 3.x or 4.0 is available)\n-  ``netmhcpan``: Local\n   `NetMHCpan <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan>`__\n   predictor\n-  ``netmhciipan``: Local\n   `NetMHCIIpan <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan>`__\n   predictor\n-  ``netmhccons``: Local\n   `NetMHCcons <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCcons>`__\n-  ``random``: Random IC50 values\n-  ``smm``: Local `SMM <http://www.mhc-pathway.net/smm>`__ predictor\n-  ``smm-pmbec``: Local\n   `SMM-PMBEC <http://www.mhc-pathway.net/smmpmbec>`__ predictor\n-  ``netmhcpan-iedb``: Use NetMHCpan via the IEDB web API\n-  ``netmhccons-iedb``: Use NetMHCcons via the IEDB web API\n-  ``smm-iedb``: Use SMM via the IEDB web API\n-  ``smm-pmbec-iedb``: Use SMM-PMBEC via the IEDB web API\n\nMHC Alleles\n~~~~~~~~~~~\n\nYou must specify the alleles to perform binding prediction for using one\nof the following flags:\n\n-  ``--mhc-alleles-file MHC_ALLELES_FILE``: Text file containing one\n   allele name per line\n-  ``--mhc-alleles MHC_ALLELES``: Comma separated list of allele names,\n   e.g. \"HLA-A02:01,HLA-B07:02\"\n\nPeptide Length\n~~~~~~~~~~~~~~\n\n-  ``--mhc-epitope-lengths MHC_EPITOPE_LENGTHS``: comma separated list\n   of integers specifying which peptide lengths to use for MHC binding\n   prediction\n\nBinding Prediction Filtering\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n-  ``--only-novel-epitopes``: Topiary will normally keep all predicted\n   epitopes, even those which occur in a given self-ligandome or don't\n   overlap a mutated region of a protein. Use this flag to drop any\n   epitopes which don't contain mutations or that occur elsewhere in the\n   self-ligandome.\n-  ``--ic50-cutoff IC50_CUTOFF``: Drop peptides with predicted IC50 nM\n   greater than this value (typical value is 500.0)\n-  ``--percentile-cutoff PERCENTILE_CUTOFF``: Drop peptides with\n   percentile rank of their predicted IC50 (among predictions for a\n   particular allele) fall below this threshold (lower values are\n   stricter filters, typical value is 2.0)\n\nMisc\n~~~~\n\n-  ``--padding-around-mutation PADDING_AROUND_MUTATION``: Include more\n   unmutated residues around the mutation (useful when not using\n   ``--only-novel-epitopes``)\n-  ``--self-filter-directory SELF_FILTER_DIRECTORY``: Directory of files\n   named by MHC allele containing a self peptide ligandome (peptides\n   which should be excluded from results)\n-  ``--skip-variant-errors``: If a particular mutation causes an\n   exception to be raised during annotation, you can skip it using this\n   flag.",
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