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Commit 8c4055a0 authored by Tim O'Donnell's avatar Tim O'Donnell
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fix

parent ef428b7d
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dist: bionic
language: python language: python
python: python:
- "3.6" - "3.6"
...@@ -17,6 +18,7 @@ before_install: ...@@ -17,6 +18,7 @@ before_install:
# Useful for debugging any issues with conda # Useful for debugging any issues with conda
- conda info -a - conda info -a
- free -m - free -m
- make -v
addons: addons:
apt: apt:
packages: packages:
......
...@@ -161,7 +161,7 @@ training data. The data we use for our released predictors can be downloaded wit ...@@ -161,7 +161,7 @@ training data. The data we use for our released predictors can be downloaded wit
It looks like this: It looks like this:
.. command-output:: .. command-output::
bzcat "$(mhcflurry-downloads path data_curated)/curated_training_data.no_mass_spec.csv.bz2" | head -n 3 bzcat "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" | head -n 3
:shell: :shell:
:nostderr: :nostderr:
......
...@@ -91,13 +91,13 @@ def test_basic(): ...@@ -91,13 +91,13 @@ def test_basic():
alleles=experiment_to_alleles, alleles=experiment_to_alleles,
n_flanks=test_df.n_flank.values, n_flanks=test_df.n_flank.values,
c_flanks=test_df.c_flank.values, c_flanks=test_df.c_flank.values,
verbose=2) verbose=2).presentation_score.values
test_df["prediction2"] = predictor.predict( test_df["prediction2"] = predictor.predict(
peptides=test_df.peptide.values, peptides=test_df.peptide.values,
sample_names=test_df.sample_id.values, sample_names=test_df.sample_id.values,
alleles=experiment_to_alleles, alleles=experiment_to_alleles,
verbose=2) verbose=2).presentation_score.values
add_prediction_cols(test_df, predictor) add_prediction_cols(test_df, predictor)
......
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