Merge pull request #1178 from griffithlab/docs

Update pVACvector docs to add more explanations about spacers and clipping

docs/pvacvector.rst

@@ -10,19 +10,25 @@ DNA vector based personalized cancer vaccines. It takes as input either a pVACse
 tsv file or a FASTA file containing peptide sequences and returns a peptide ordering that
 minimizes the effects of junctional epitopes (that may create novel peptides)
 between the sequences. It does this by using the core pVACseq services to
-predict the binding scores for each junctional peptide separated by a spacer amino acid
-sequence that may help to eliminate junctional epitopes. The list of spacers
-to be tested is specified using the ``--spacers`` parameter. Peptide combinations without a
-spacer can be tested by including ``None`` in the list of spacers.
+predict the binding scores for each junctional peptide.
 
-Peptide junctions are tested with
-each spacer in the order that they are specified. If a valid peptide ordering
-is found that doesn't result in any well-binding junction epitopes, that
-ordering is returned. No other spacer are tested, even if they could
-potentially result in better junction scores. This reduces runtime.
-If no valid path is found, the next spacer in the input list is tested.
-The default spacer amino acid sequences are "None", "AAY", "HHHH", "GGS", "GPGPG", "HHAA",
-"AAL", "HH", "HHC", "HHH", "HHHD", "HHL", "HHHC".
+Running pVACvector with spacer amino acid sequences may help eliminate junctional
+epitopes. The list of spacers to be tested is specified using the ``--spacers``
+parameter. Peptide combinations without a spacer can be tested by including
+``None`` in the list of spacers. The default spacer amino acid sequences are
+"None", "AAY", "HHHH", "GGS", "GPGPG", "HHAA", "AAL", "HH", "HHC", "HHH", "HHHD",
+"HHL", "HHHC". Peptide junctions are tested with each spacer in the order that
+they are specified. If a tested spacers results in a valid junction without any
+well-binding junction epitopes, that junction will not be tested with any
+other spacers, even if a different spacer could potentially result in better
+junction scores. This reduces runtime. If a tested spacer for a junction doesn't
+yield a valid junction (i.e., there are well-binding junction epitopes) the junction
+is tested wtih the next spacer in the input list.
+
+If, after testing all spacers, no valid path is found, clipped versions of
+peptides are tested by removing leading and/or trailing amino acids and
+constructing junctions with the clipped peptides. The maximum number of amino
+acids to clip is controlled by the ``--max-clip-length`` argument.
 
 The final vaccine ordering is
 achieved through a simulated annealing procedure that returns a near-optimal

docs/pvacvector/run.rst

@@ -25,6 +25,24 @@ of a design, while more conservative settings of 1000nM and lowest/best binding
 value (``--top-score-metric lowest``) will give more confidence that there are
 no junctional neoepitopes.
 
+Running pVACvector with spacer amino acid sequences may help eliminate junctional
+epitopes. The list of spacers to be tested is specified using the ``--spacers``
+parameter. Peptide combinations without a spacer can be tested by including
+``None`` in the list of spacers. The default spacer amino acid sequences are
+"None", "AAY", "HHHH", "GGS", "GPGPG", "HHAA", "AAL", "HH", "HHC", "HHH", "HHHD",
+"HHL", "HHHC". Peptide junctions are tested with each spacer in the order that
+they are specified. If a tested spacers results in a valid junction without any
+well-binding junction epitopes, that junction will not be tested with any
+other spacers, even if a different spacer could potentially result in better
+junction scores. This reduces runtime. If a tested spacer for a junction doesn't
+yield a valid junction (i.e., there are well-binding junction epitopes) the junction
+is tested wtih the next spacer in the input list.
+
+If, after testing all spacers, no valid path is found, clipped versions of
+peptides are tested by removing leading and/or trailing amino acids and
+constructing junctions with the clipped peptides. The maximum number of amino
+acids to clip is controlled by the ``--max-clip-length`` argument.
+
 Our current recommendation is to run pVACvector several different ways, and
 choose the path resulting from the most conservative set of parameters.