Merge 5871c98 into 7c4b383

.gitignore

@@ -24,3 +24,4 @@ build/
 dist/
 .DS_Store
 docs/.DS_Store
+.idea/

docs/pvacsplice.rst

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+pVACsplice
+========================
+
+pVACsplice predicts neoantigens for novel junctions created from tumor-specific alternative splicing patterns.
+
+.. toctree::
+   :glob:
+
+   pvacsplice/input_file_prep
+   pvacsplice/getting_started
+   pvacsplice/run

docs/pvacsplice/getting_started.rst

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+Getting Started
+===============
+
+pVACsplice provides a set of example data to show the expected format of input and output files. You can download the data set by running the ``pvacsplice download_example_data`` command.
+
+The example data output can be reproduced by running the following command:
+
+.. code-block:: none
+
+   pvacsplice run \
+   <example_data_dir>/input_junctions.tsv \
+   <sample_name> \
+   HLA-A*01:01,HLA-A*02:01,HLA-B*15:01,HLA-B*57:01,HLA-C*03:03,HLA-C*06:02 \
+   all_class_i \
+   <output_dir> \
+   annotated_variants.vcf \
+   ref.fa
+
+A detailed description of all command options can be found on the following page.

docs/pvacsplice/input_file_prep.rst

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+Input File Preparation
+======================
+
+The main input files to the pVACsplice pipeline are an annotated VCF file and a RegTools output file (tsv).
+
+Step 1: Annotate VCF file
+******************************
+
+Please see the `pVACseq Input File Preparation <https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep.html>`_ for instructions on how to prepare an annotated VCF file.
+
+Step 2: Run RegTools
+********************
+
+RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. To run pVACsplice, you must first run RegTools ``cis-splice-effects identify`` to generate a list of non-canonical splicing junctions created from *cis*-acting regulatory variants. The output tsv file (-o option) is an input to pVACsplice. Here is an example command:
+
+.. code-block:: none
+
+   regtools cis-splice-effects identify \
+   -o <output tsv file> \
+   -s <rna_strand> \
+   annotated_variants.vcf \ 
+   rna_alignments.bam \ 
+   ref.fa \
+   annotations.gtf
+
+Please see the `RegTools documentation
+<https://regtools.readthedocs.io/en/latest/commands/cis-splice-effects-identify/>`_
+for more information.
+
+
+

docs/pvacsplice/run.rst

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+Usage
+=========================
+
+.. warning::
+   Using a local IEDB installation is strongly recommended for larger datasets
+   or when the making predictions for many alleles, epitope lengths, or
+   prediction algorithms. More information on how to install IEDB locally can
+   be found on the :ref:`Installation <iedb_install>` page.
+
+   .. program-output:: pvacsplice run -h
+
+..  .. argparse::
+        :module: tools.pvacsplice.run
+        :func: define_parser
+        :prog: pvacsplice run