From 6b592c812fa0bd12da730c313aae9aa7f75bd3a0 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 17 Apr 2017 17:58:27 -0400
Subject: [PATCH] update
---
mhcflurry/antigen_presentation/presentation_model.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/mhcflurry/antigen_presentation/presentation_model.py b/mhcflurry/antigen_presentation/presentation_model.py
index 73c1f688..33e3e709 100644
--- a/mhcflurry/antigen_presentation/presentation_model.py
+++ b/mhcflurry/antigen_presentation/presentation_model.py
@@ -422,6 +422,8 @@ class PresentationModel(object):
assert 'experiment_name' in peptides_df.columns
assert 'hit' in peptides_df.columns
+ peptides_df = peptides_df.copy()
+
peptides_df["prediction"] = self.predict(peptides_df)
top_n = float(peptides_df.hit.sum())
@@ -432,8 +434,13 @@ class PresentationModel(object):
}
else:
ranks = peptides_df.prediction.rank(ascending=False)
+ hit_indices = ranks[peptides_df.hit > 0].values
+ hit_lengths = peptides_df.peptide[
+ peptides_df.hit > 0
+ ].str.len().values
result = {
- 'hit_indices': numpy.sort(ranks[peptides_df.hit > 0].values),
+ 'hit_indices': hit_indices,
+ 'hit_lengths': hit_lengths,
'total_peptides': len(peptides_df),
}
result['score'] = (
--
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