From ef428b7db50df356ed5a8be728d9b66d701019b0 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 20 Mar 2020 20:01:17 -0400
Subject: [PATCH] docs
---
docs/commandline_tools.rst | 34 ++++++++++++++++++++++++++++++++++
docs/commandline_tutorial.rst | 8 ++++----
docs/example.fasta | 6 ++----
docs/intro.rst | 4 ++--
4 files changed, 42 insertions(+), 10 deletions(-)
diff --git a/docs/commandline_tools.rst b/docs/commandline_tools.rst
index 20f7cbe5..dc92a15c 100644
--- a/docs/commandline_tools.rst
+++ b/docs/commandline_tools.rst
@@ -18,4 +18,38 @@ See also the :ref:`tutorial <commandline_tutorial>`.
.. autoprogram:: mhcflurry.downloads_command:parser
:prog: mhcflurry-downloads
+.. _mhcflurry-class1-train-allele-specific-models:
+
+.. autoprogram:: mhcflurry.train_allele_specific_models_command:parser
+ :prog: mhcflurry-class1-train-allele-specific-models
+
+.. _mhcflurry-class1-select-allele-specific-models:
+
+.. autoprogram:: mhcflurry.select_allele_specific_models_command:parser
+ :prog: mhcflurry-class1-select-allele-specific-models
+
+.. _mhcflurry-class1-train-pan-allele-models:
+
+.. autoprogram:: mhcflurry.train_pan_allele_models_command:parser
+ :prog: mhcflurry-class1-train-pan-allele-models
+
+.. _mhcflurry-class1-select-pan-allele-models:
+
+.. autoprogram:: mhcflurry.select_pan_allele_models_command:parser
+ :prog: mhcflurry-class1-select-pan-allele-models
+
+.. _mhcflurry-class1-train-processing-models:
+
+.. autoprogram:: mhcflurry.train_processing_models_command:parser
+ :prog: mhcflurry-class1-train-processing-models
+
+.. _mhcflurry-class1-select-processing-models:
+
+.. autoprogram:: mhcflurry.select_processing_models_command:parser
+ :prog: mhcflurry-class1-select-processing-models
+
+.. _mhcflurry-class1-train-presentation-models:
+
+.. autoprogram:: mhcflurry.train_presentation_models_command:parser
+ :prog: mhcflurry-class1-train-presentation-models
diff --git a/docs/commandline_tutorial.rst b/docs/commandline_tutorial.rst
index 2014ec55..874f6860 100644
--- a/docs/commandline_tutorial.rst
+++ b/docs/commandline_tutorial.rst
@@ -33,7 +33,7 @@ as well as an antigen processing (AP) predictor.
.. note::
The code we use for *generating* the downloads is in the
- ``downloads_generation`` directory in the repository.
+ ``downloads_generation`` directory in the repository (https://github.com/openvax/mhcflurry/tree/master/downloads-generation)
Generating predictions
@@ -99,7 +99,7 @@ sequences:
.. literalinclude:: /example.fasta
Here's the ``mhcflurry-predict-scan`` invocation to scan the proteins for
-binders to either of two MHC I genotypes:
+binders to either of two MHC I genotypes (using a 100 nM threshold):
.. command-output::
mhcflurry-predict-scan
@@ -107,8 +107,8 @@ binders to either of two MHC I genotypes:
--alleles
HLA-A*02:01,HLA-A*03:01,HLA-B*57:01,HLA-B*45:01,HLA-C*02:02,HLA-C*07:02
HLA-A*01:01,HLA-A*02:06,HLA-B*44:02,HLA-B*07:02,HLA-C*01:02,HLA-C*03:01
- --results-filtered affinity_percentile
- --threshold-affinity-percentile 1.0
+ --results-filtered affinity
+ --threshold-affinity 100
:nostderr:
See the :ref:`mhcflurry-predict-scan` docs for more options.
diff --git a/docs/example.fasta b/docs/example.fasta
index ea095115..aa862345 100644
--- a/docs/example.fasta
+++ b/docs/example.fasta
@@ -1,6 +1,4 @@
>protein1
-MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQV
-EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHH
+MSSSSTPVCPNGPGNCQV
>protein2
-VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGA
-ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC
+MVENKRLLEGMEMIFGQVIPGA
diff --git a/docs/intro.rst b/docs/intro.rst
index 5b5f3581..e1ebba0c 100644
--- a/docs/intro.rst
+++ b/docs/intro.rst
@@ -2,7 +2,7 @@ Introduction and setup
=======================
MHCflurry is an open source package for peptide/MHC I binding affinity prediction. It
-attempts to provide competitive accuracy with a fast and documented implementation.
+aims to provide competitive accuracy with a fast and documented implementation.
You can download pre-trained MHCflurry models fit to mass spec-identified MHC I
ligands and peptide/MHC affinity measurements deposited in IEDB (plus a few other
@@ -63,7 +63,7 @@ tensorflow.
.. code-block:: shell
- $ conda create -q -n mhcflurry-env python=3.6 tensorflow
+ $ conda create -q -n mhcflurry-env python=3.6 'tensorflow<2.0.0'
$ source activate mhcflurry-env
Then continue as above:
--
GitLab