From 18d9460da3fe4a1673e883adacd6e9c0deb80ee8 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 4 Oct 2019 12:48:43 -0400
Subject: [PATCH] fix
---
.../data_mass_spec_benchmark/run_predictors.py | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/run_predictors.py b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
index d5eabd07..d74d2a80 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_predictors.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
@@ -238,10 +238,8 @@ def run(argv=sys.argv[1:]):
if args.reuse_predictions:
# Allocating this here to hit any memory errors as early as possible.
- is_null_matrix = pandas.DataFrame(
- columns=alleles,
- index=result_df.index,
- dtype="int8")
+ is_null_matrix = numpy.ones(
+ shape=(result_df.shape[0], len(alleles)), dtype="int8")
for dirname in args.reuse_predictions:
if not dirname:
@@ -255,19 +253,20 @@ def run(argv=sys.argv[1:]):
# We rerun any alleles have nulls for any kind of values
# (e.g. affinity, percentile rank, elution score).
- for (allele, sub_df) in manifest_df.groupby("allele"):
- is_null_matrix[allele] = result_df[sub_df.col.values].isnull().any(1)
- print("Fraction null", is_null_matrix.values.mean())
+ for (i, allele) in enumerate(alleles):
+ sub_df = manifest_df.loc[manifest_df.allele == allele]
+ is_null_matrix[:, i] = result_df[sub_df.col.values].isnull().any(1)
+ print("Fraction null", is_null_matrix.mean())
print("Computing blocks.")
start = time.time()
- blocks = blocks_of_ones(is_null_matrix.values)
+ blocks = blocks_of_ones(is_null_matrix)
print("Found %d blocks in %f sec." % (
len(blocks), (time.time() - start)))
work_items = []
for (row_index1, col_index1, row_index2, col_index2) in blocks:
- block_alleles = is_null_matrix.columns[col_index1 : col_index2 + 1]
+ block_alleles = alleles[col_index1 : col_index2 + 1]
block_peptides = result_df.index[row_index1 : row_index2 + 1]
print("Block: ", row_index1, col_index1, row_index2, col_index2)
--
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