Upgrade to version 5.0.0

griffithlab · Dec 18, 2024 · 0a46ede · 0a46ede
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diff --git a/docs/conf.py b/docs/conf.py
@@ -68,9 +68,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.4'
+version = '5.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.4.1'
+release = '5.0.0'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

diff --git a/docs/images/pVACsplice_logo_trans-bg_v4b.png b/docs/images/pVACsplice_logo_trans-bg_v4b.png
diff --git a/docs/images/pVACtools_main-figure_v8.png b/docs/images/pVACtools_main-figure_v8.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -25,7 +25,7 @@ tools:
    users in reviewing, exploring and prioritizing neoantigens from the results of
    pVACtools processes for personalized cancer vaccine design.
 
-.. image:: images/pVACtools_main-figure_v7.png
+.. image:: images/pVACtools_main-figure_v8.png
     :align: center
     :alt: pVACtools immunotherapy workflow
 
@@ -57,22 +57,42 @@ Contents
    contact
    mailing_list
 
-New in Release |release|
+New in Version |version|
 ------------------------
 
-This is a bugfix release. It fixes the following problem(s):
-
-- Previously, pVACview would add an additional header line to Excel spreadsheets
-  when exporting a TSV. This has been fixed so that the first line in the spreadsheet
-  is the actual header line.
-  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1143
-- One of the pVACview figures used to describe various anchor scenarios has been updated
-  so that the ordering of the scenarios is consistent with other figures and descriptions
-  throughout. Screenshots and documentation has been updated appropriately.
-  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1144
-- The class II pVACview demo data was out-of-date and not reflecting recent updates to the
-  HLA alpha-beta chain handling. This file has now been updated.
-  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1145
+This is a major version release. Please note that pVACtools 5.0 is not guaranteed to be
+backwards-compatible and certain changes could break old workflows.
+
+New Tools
+_________
+
+This release adds a new tool, pVACsplice, for prediction neoantigens from
+splice sites. Please see the :ref:`full tool documentation <pvacsplice>` for more information.
+by @mrichters in https://github.com/griffithlab/pVACtools/pull/911
+
+New Features
+____________
+
+- This release refactors the pVACvector graph building algorithm in order to increase the probability
+  for finding a solution and reduce the number of iterations needed before a solution is found. Please
+  see the PR describtion for the full details. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1163
+- Add a new ``--aggregate-inclusion-count-limit`` parameter to set the maximum number of epitopes
+  to include in the metrics.json detailed data for variants that have a large number of candidate
+  neoantigens (e.g., frameshifts). by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1147
+- Add support for additional alleles that weren't previously supported, includings ones for dog,
+  mouse, and MHC class II. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1148
+
+Bugfixes
+________
+
+- This relase fixes a bug with the ``--agregate-inclusion-binding-threshold`` which would not be used if
+  the ``--allele-specific-binding-thresholds`` flag was set. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1147
+- The pVACview percentile plots have been updated to include percentiles from elution and immunogenicity
+  algorithms. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1149
+- This release fixes a bug where the incorrect neoantigen fasta entry may be used for the reference proteome
+  search if there were multiple variants or alt alleles located at the same genomic position. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1153
+- Add additional trailing amino acids for frameshift insertions when creating fasta in order to capture a
+  matched wildtype entry in large repetitive regions. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1155
 
 Past release notes can be found on our :ref:`releases` page.
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -90,8 +90,8 @@ Download the archives for `class II <http://tools.iedb.org/mhcii/download/>`_ an
 .. code-block:: none
 
    apt-get update && apt-get install -y tcsh gawk
-   wget https://downloads.iedb.org/tools/mhcii/3.1.11/IEDB_MHC_II-3.1.11.tar.gz
-   tar -zxvf IEDB_MHC_II-3.1.11.tar.gz
+   wget https://downloads.iedb.org/tools/mhcii/3.1.12/IEDB_MHC_II-3.1.12.tar.gz
+   tar -zxvf IEDB_MHC_II-3.1.12.tar.gz
    cd mhc_ii
    ./configure.py
 

diff --git a/docs/pvacsplice.rst b/docs/pvacsplice.rst
@@ -1,3 +1,10 @@
+.. image:: images/pVACsplice_logo_trans-bg_v4b.png
+    :align: right
+    :alt: pVACsplice logo
+    :width: 175px
+
+.. _pvacsplice:
+
 pVACsplice
 ==========
 

diff --git a/docs/pvacsplice/additional_commands.rst b/docs/pvacsplice/additional_commands.rst
@@ -1,6 +1,7 @@
-.. .. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
     :align: right
-    :alt: pVACseq logo
+    :alt: pVACsplice logo
+    :width: 175px
 
 Additional Commands
 ===================

diff --git a/docs/pvacsplice/features.rst b/docs/pvacsplice/features.rst
@@ -1,6 +1,7 @@
-.. .. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
     :align: right
     :alt: pVACsplice logo
+    :width: 175px
 
 Features
 ========

diff --git a/docs/pvacsplice/filter_commands.rst b/docs/pvacsplice/filter_commands.rst
@@ -1,6 +1,7 @@
-.. .. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
     :align: right
-    :alt: pVACseq logo
+    :alt: pVACsplice logo
+    :width: 175px
 
 .. _pvacsplice_filter_commands:
 

diff --git a/docs/pvacsplice/getting_started.rst b/docs/pvacsplice/getting_started.rst
@@ -1,3 +1,8 @@
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
+    :align: right
+    :alt: pVACsplice logo
+    :width: 175px
+
 Getting Started
 ===============
 

diff --git a/docs/pvacsplice/input_file_prep.rst b/docs/pvacsplice/input_file_prep.rst
@@ -1,3 +1,8 @@
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
+    :align: right
+    :alt: pVACsplice logo
+    :width: 175px
+
 .. _pvacsplice_prerequisites_label:
 
 Input File Preparation

diff --git a/docs/pvacsplice/optional_downstream_analysis_tools.rst b/docs/pvacsplice/optional_downstream_analysis_tools.rst
@@ -1,6 +1,7 @@
-.. .. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
     :align: right
     :alt: pVACsplice logo
+    :width: 175px
 
 .. _pvacsplice_optional_downstream_analysis_tools_label:
 

diff --git a/docs/pvacsplice/output_files.rst b/docs/pvacsplice/output_files.rst
@@ -1,6 +1,7 @@
-.. .. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
     :align: right
-    :alt: pVACseq logo
+    :alt: pVACsplice logo
+    :width: 175px
 
 .. _pvacsplice_output_files:
 

diff --git a/docs/pvacsplice/run.rst b/docs/pvacsplice/run.rst
@@ -1,3 +1,8 @@
+.. image:: ../images/pVACsplice_logo_trans-bg_v4b.png
+    :align: right
+    :alt: pVACsplice logo
+    :width: 175px
+
 Usage
 =====
 

diff --git a/docs/releases.rst b/docs/releases.rst
@@ -21,3 +21,4 @@ Release Notes
    releases/4_2
    releases/4_3
    releases/4_4
+   releases/5_0
diff --git a/docs/releases/5_0.rst b/docs/releases/5_0.rst
@@ -0,0 +1,40 @@
+Version 5.0
+===========
+
+Version 5.0.0
+-------------
+
+This version adds the following features, outlined below. Please note that
+pVACtools 5.0 is not guaranteed to be backwards-compatible and certain changes
+could break old workflows.
+
+New Tools
+_________
+
+This release adds a new tool, pVACsplice, for prediction neoantigens from
+splice sites. Please see the :ref:`full tool documentation <pvacsplice>` for more information.
+by @mrichters in https://github.com/griffithlab/pVACtools/pull/911
+
+New Features
+____________
+
+- This release refactors the pVACvector graph building algorithm in order to increase the probability
+  for finding a solution and reduce the number of iterations needed before a solution is found. Please
+  see the PR describtion for the full details. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1163
+- Add a new ``--aggregate-inclusion-count-limit`` parameter to set the maximum number of epitopes
+  to include in the metrics.json detailed data for variants that have a large number of candidate
+  neoantigens (e.g., frameshifts). by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1147
+- Add support for additional alleles that weren't previously supported, includings ones for dog,
+  mouse, and MHC class II. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1148
+
+Bugfixes
+________
+
+- This relase fixes a bug with the ``--agregate-inclusion-binding-threshold`` which would not be used if
+  the ``--allele-specific-binding-thresholds`` flag was set. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1147
+- The pVACview percentile plots have been updated to include percentiles from elution and immunogenicity
+  algorithms. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1149
+- This release fixes a bug where the incorrect neoantigen fasta entry may be used for the reference proteome
+  search if there were multiple variants or alt alleles located at the same genomic position. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1153
+- Add additional trailing amino acids for frameshift insertions when creating fasta in order to capture a
+  matched wildtype entry in large repetitive regions. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1155
diff --git a/pvactools/lib/post_processor.py b/pvactools/lib/post_processor.py
@@ -131,6 +131,7 @@ def aggregate_all_epitopes(self):
                 percentile_threshold=self.percentile_threshold,
                 allele_specific_binding_thresholds=self.allele_specific_binding_thresholds,
                 aggregate_inclusion_binding_threshold=self.aggregate_inclusion_binding_threshold,
+                aggregate_inclusion_count_limit=self.aggregate_inclusion_count_limit,
                 top_score_metric=self.top_score_metric,
                 trna_vaf=self.trna_vaf,
                 trna_cov=self.trna_cov,

diff --git a/pvactools/tools/pvacview/server.R b/pvactools/tools/pvacview/server.R
@@ -24,7 +24,7 @@ options(shiny.port = 3333)
 server <- shinyServer(function(input, output, session) {
   ## pVACtools version
 
-  output$version <- renderText({"pVACtools version 4.4.0"})
+  output$version <- renderText({"pVACtools version 5.0.0"})
 
   ##############################DATA UPLOAD TAB###################################
   ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus)

diff --git a/setup.py b/setup.py
@@ -56,7 +56,7 @@
 
 setup(
     name="pvactools",
-    version="4.4.1",
+    version="5.0.0",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",