From 8b08d48256de994aadacbc0cf3a5e0422d67e818 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 8 Mar 2020 16:30:56 -0400
Subject: [PATCH] update variants
---
.../data_evaluation/GENERATE.sh | 2 +-
mhcflurry/class1_presentation_predictor.py | 35 ++++++++++++++++++-
mhcflurry/downloads.yml | 2 +-
3 files changed, 36 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/data_evaluation/GENERATE.sh b/downloads-generation/data_evaluation/GENERATE.sh
index 1e0ec683..8a562dc4 100755
--- a/downloads-generation/data_evaluation/GENERATE.sh
+++ b/downloads-generation/data_evaluation/GENERATE.sh
@@ -143,7 +143,7 @@ do
echo bzip2 -f "$(pwd)/benchmark.multiallelic.production.$kind.csv" >> commands/multiallelic.production.$kind.sh
fi
- for variant in no_additional_ms compact_peptide affinity_only no_pretrain single_hidden_no_pretrain
+ for variant in no_additional_ms compact_peptide affinity_only no_pretrain single_hidden_no_pretrain 500nm
do
if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.${variant}.$kind.csv.bz2" ]
then
diff --git a/mhcflurry/class1_presentation_predictor.py b/mhcflurry/class1_presentation_predictor.py
index ef3f5e48..30e535bf 100644
--- a/mhcflurry/class1_presentation_predictor.py
+++ b/mhcflurry/class1_presentation_predictor.py
@@ -252,6 +252,22 @@ class Class1PresentationPredictor(object):
n_flanks=None,
c_flanks=None,
verbose=1):
+ """
+ Predict presentation scores across a set of peptides.
+
+ Parameters
+ ----------
+ peptides : list of string, or EncodableSequences
+ alleles : list of string or string -> string dict
+ experiment_names :
+ n_flanks
+ c_flanks
+ verbose
+
+ Returns
+ -------
+
+ """
return self.predict_to_dataframe(
peptides=peptides,
alleles=alleles,
@@ -273,7 +289,7 @@ class Class1PresentationPredictor(object):
verbose=1,
throw=True):
"""
- Predict across protein sequences.
+ Predict presentation across protein sequences.
Parameters
----------
@@ -439,6 +455,23 @@ class Class1PresentationPredictor(object):
include_affinity_percentile=False,
verbose=1,
throw=True):
+ """
+
+ Parameters
+ ----------
+ peptides
+ alleles
+ experiment_names
+ n_flanks
+ c_flanks
+ include_affinity_percentile
+ verbose
+ throw
+
+ Returns
+ -------
+
+ """
if isinstance(peptides, string_types):
raise TypeError("peptides must be a list not a string")
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 7a1fb56c..4ec26a95 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -37,7 +37,7 @@ releases:
default: false
- name: models_class1_pan_variants
- url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan_variants.selected.20200109.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan_variants.selected.20200307.tar.bz2
default: false
- name: models_class1_processing_variants
--
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