diff --git a/README.md b/README.md
index dbbeb1f1305746d92e3fc3198621f5b75029e657..b9dfadcc124ddd4734826551dcf2c23364031802 100644
--- a/README.md
+++ b/README.md
@@ -19,10 +19,10 @@ Download, Normalize, and Combine Training Data:
(make sure you have `wget` available, e.g. `brew install wget` on Mac OS X)
```
-scripts/download-iedb.sh
-scripts/download-peters-2013-dataset.sh
-scripts/create-iedb-class1-dataset.py
-scripts/create-combined-class1-dataset.py
+script/download-iedb.sh
+script/download-peters-2013-dataset.sh
+script/create-iedb-class1-dataset.py
+script/create-combined-class1-dataset.py
```
## Train Neural Network Models
diff --git a/mhcflurry/class1_allele_specific_hyperparameters.py b/mhcflurry/class1_allele_specific_hyperparameters.py
index e1e0c36650d3f3e8dba54a68725de0e3de81301d..33e15cdba88b2b7ea3dd5a52ef7a4925606682c0 100644
--- a/mhcflurry/class1_allele_specific_hyperparameters.py
+++ b/mhcflurry/class1_allele_specific_hyperparameters.py
@@ -36,46 +36,50 @@ def add_hyperparameter_arguments_to_parser(parser):
"--training-epochs",
type=int,
default=N_EPOCHS,
- help="Number of training epochs")
+ help="Number of training epochs. Default: %(default)s")
parser.add_argument(
"--initialization",
default=INITIALIZATION_METHOD,
- help="Initialization for neural network weights")
+ help="Initialization for neural network weights Default: %(default)s")
parser.add_argument(
"--activation",
default=ACTIVATION,
- help="Activation function for neural network layers")
+ help="Activation function for neural network layers. "
+ "Default: %(default)s")
parser.add_argument(
"--embedding-size",
type=int,
default=EMBEDDING_DIM,
- help="Size of vector representations for embedding amino acids")
+ help="Size of vector representations for embedding amino acids. "
+ "Default: %(default)s")
parser.add_argument(
"--hidden-layer-size",
type=int,
default=HIDDEN_LAYER_SIZE,
- help="Size of hidden neural network layer")
+ help="Size of hidden neural network layer. Default: %(default)s")
parser.add_argument(
"--dropout",
type=float,
default=DROPOUT_PROBABILITY,
- help="Dropout probability after neural network layers")
+ help="Dropout probability after neural network layers. "
+ "Default: %(default)s")
parser.add_argument(
"--max-ic50",
type=float,
default=MAX_IC50,
- help="Largest IC50 represented by neural network output")
+ help="Largest IC50 represented by neural network output. "
+ "Default: %(default)s")
parser.add_argument(
"--learning-rate",
type=float,
default=0.001,
- help="Learning rate for training neural network")
+ help="Learning rate for training neural network. Default: %(default)s")
return parser
diff --git a/requirements.txt b/requirements.txt
index d30114246bb4a1bb9b2bbf1dfb51e61c6d586486..f1babbeae2cfeb74c412b1c5741d4bce989a45fa 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
numpy>= 1.7
pandas>=0.13.1
appdirs
-theano
+theano>=0.8.2
keras<1.0
h5py
cherrypy
diff --git a/script/create-combined-class1-dataset.py b/script/create-combined-class1-dataset.py
index c8880de4de331c57f236624c46c8702ca7c84aa7..fbfad25aafc6e9a9811e7767b0dd527b93388fd5 100755
--- a/script/create-combined-class1-dataset.py
+++ b/script/create-combined-class1-dataset.py
@@ -41,7 +41,7 @@ IEDB_PICKLE_PATH = join(CLASS1_DATA_DIRECTORY, IEDB_PICKLE_FILENAME)
KIM_2013_CSV_FILENAME = "bdata.20130222.mhci.public.1.txt"
-parser = argparse.ArgumentParser()
+parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument(
"--ic50-fraction-tolerance",
@@ -49,40 +49,46 @@ parser.add_argument(
type=float,
help=(
"How much can the IEDB and NetMHCpan IC50 differ and still be"
- " considered compatible (as a fraction of the NetMHCpan value)"))
+ " considered compatible (as a fraction of the NetMHCpan value). "
+ "Default: %(default)s"))
parser.add_argument(
"--min-assay-overlap-size",
type=int,
default=1,
- help="Minimum number of entries overlapping between IEDB assay and NetMHCpan data")
+ help="Minimum number of entries overlapping between IEDB assay and "
+ "NetMHCpan data. Default: %(default)s")
parser.add_argument(
"--min-assay-fraction-same",
type=float,
- help="Minimum fraction of peptides whose IC50 values agree with the NetMHCpan data",
+ help="Minimum fraction of peptides whose IC50 values agree with the "
+ "NetMHCpan data. Default: %(default)s",
default=0.9)
parser.add_argument(
"--iedb-pickle-path",
default=IEDB_PICKLE_PATH,
- help="Path to .pickle file containing dictionary of IEDB assay datasets")
+ help="Path to .pickle file containing dictionary of IEDB assay datasets. "
+ "Default: %(default)s")
parser.add_argument(
"--netmhcpan-csv-path",
default=KIM_2013_CSV_FILENAME,
- help="Path to CSV with NetMHCpan dataset from 2013 Peters paper")
+ help="Path to CSV with NetMHCpan dataset from 2013 Peters paper. "
+ "Default: %(default)s")
parser.add_argument(
"--output-dir",
default=CLASS1_DATA_DIRECTORY,
- help="Path to directory where output CSV should be written")
+ help="Path to directory where output CSV should be written. "
+ "Default: %(default)s")
parser.add_argument(
"--output-csv-filename",
default=CLASS1_DATA_CSV_FILENAME,
- help="Name of combined CSV file")
+ help="Name of combined CSV file. Default: %(default)s")
parser.add_argument(
"--extra-dataset-csv-path",
diff --git a/script/create-iedb-class1-dataset.py b/script/create-iedb-class1-dataset.py
index f6f147c10be20a07820d1ca92c4b7d7ffd0315cf..d059909bf072e5f8e3acd80ff69d4c30f07cee2b 100755
--- a/script/create-iedb-class1-dataset.py
+++ b/script/create-iedb-class1-dataset.py
@@ -33,25 +33,27 @@ from mhcflurry.paths import CLASS1_DATA_DIRECTORY
IEDB_SOURCE_FILENAME = "mhc_ligand_full.csv"
PICKLE_OUTPUT_FILENAME = "iedb_human_class1_assay_datasets.pickle"
-parser = argparse.ArgumentParser()
+parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument(
"--input-csv",
default=IEDB_SOURCE_FILENAME,
- help="CSV file with IEDB's MHC binding data")
+ help="CSV file with IEDB's MHC binding data. Default: %(default)s")
parser.add_argument(
"--output-dir",
default=CLASS1_DATA_DIRECTORY,
- help="Directory to write output pickle file")
+ help="Directory to write output pickle file. Default: %(default)s")
parser.add_argument(
"--output-pickle-filename",
default=PICKLE_OUTPUT_FILENAME,
- help="Path to .pickle file containing dictionary of IEDB assay datasets")
+ help="Path to .pickle file containing dictionary of IEDB assay datasets. "
+ "Default: %(default)s")
parser.add_argument(
"--alleles",
+ metavar="ALLELE",
nargs="+",
default=[],
help="Restrict dataset to specified alleles")
diff --git a/script/mhcflurry-train-class1-allele-specific-models.py b/script/mhcflurry-train-class1-allele-specific-models.py
index 3995808d6499a47a8d2d0e1abc875f149c04b506..dab6976812c4b17e7741fa590dc3a183aaffd7a5 100755
--- a/script/mhcflurry-train-class1-allele-specific-models.py
+++ b/script/mhcflurry-train-class1-allele-specific-models.py
@@ -61,12 +61,14 @@ parser = argparse.ArgumentParser()
parser.add_argument(
"--binding-data-csv",
default=CSV_PATH,
- help="CSV file with 'mhc', 'peptide', 'peptide_length', 'meas' columns")
+ help="CSV file with 'mhc', 'peptide', 'peptide_length', 'meas' columns. "
+ "Default: %(default)s")
parser.add_argument(
"--output-dir",
default=CLASS1_MODEL_DIRECTORY,
- help="Output directory for allele-specific predictor HDF weights files")
+ help="Output directory for allele-specific predictor HDF weights files. "
+ "Default: %(default)s")
parser.add_argument(
"--overwrite",
@@ -77,11 +79,15 @@ parser.add_argument(
parser.add_argument(
"--min-samples-per-allele",
default=5,
- help="Don't train predictors for alleles with fewer samples than this",
+ metavar="N",
+ help="Don't train predictors for alleles with fewer than N samples. "
+ "Default: %(default)s",
type=int)
parser.add_argument(
"--alleles",
+ metavar="ALLELE",
+ help="Alleles to train",
default=[],
nargs="+",
type=normalize_allele_name)
diff --git a/setup.py b/setup.py
index 382a5786e33c789363c9c5e4b7dd9d6101096186..3078c409d8f7048aa5abada27bd14469ed5ffa89 100644
--- a/setup.py
+++ b/setup.py
@@ -64,7 +64,7 @@ if __name__ == '__main__':
'numpy>=1.7',
'pandas>=0.13.1',
'appdirs',
- 'theano',
+ 'theano>=0.8.2',
'keras',
'fancyimpute',
'scikit-learn',