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def test_deepsea():
model = kipoi.get_model("DeepSEA/variantEffects")
mie = ModelInfoExtractor(model, SeqIntervalDl)
def test_var_eff_pred_varseq(tmpdir):
model_name = "DeepSEA/variantEffects"
if INSTALL_REQ:
install_model_requirements(model_name, "kipoi", and_dataloaders=True)
#
model = kipoi.get_model(model_name, source="kipoi")
# The preprocessor
Dataloader = SeqIntervalDl
#
dataloader_arguments = {"intervals_file": "example_files/intervals.bed",
"fasta_file": "example_files/hg38_chr22.fa",
"required_seq_len": 1000, "alphabet_axis": 1, "dummy_axis": 2, "label_dtype": str}
dataloader_arguments = {k: model.source_dir + "/" + v if isinstance(v, str) else v for k, v in
dataloader_arguments.items()}
vcf_path = "tests/data/variants.vcf"
out_vcf_fpath = str(tmpdir.mkdir("variants_generated", ).join("out.vcf"))
#
vcf_path = kipoi_veff.ensure_tabixed_vcf(vcf_path)
model_info = kipoi_veff.ModelInfoExtractor(model, Dataloader)
writer = kipoi_veff.VcfWriter(
model, vcf_path, out_vcf_fpath, standardise_var_id=True)
def test_ref_seq():
# Get pure fasta predictions
model_dir = model_root + "./"
model = kipoi.get_model(model_dir, source="dir")
# The preprocessor
Dataloader = kipoi.get_dataloader_factory(model_dir, source="dir")
dataloader_arguments = {
"fasta_file": "/nfs/research1/stegle/users/rkreuzhu/opt/manuscript_code/data/raw/dataloader_files/shared/hg19.fa",
"intervals_file": "test_files/test_encode_roadmap.bed"
}
# predict using results
preds = model.pipeline.predict(dataloader_arguments)
#
res_orig = pd.read_csv("/nfs/research1/stegle/users/rkreuzhu/deeplearning/Basset/data/test_encode_roadmap_short_pred.txt", "\t", header=None)
assert np.isclose(preds, res_orig.values, atol=1e-3).all()
def __init__(self, x=1):
#self.embed = kipoi.get_model("SeqVec/embedding")
#self.struct = kipoi.get_model("SeqVec/embedding2structure")
self.embed = kipoi.get_model("/home/mheinzinger/tmp/models/SeqVec/embedding")
self.struct = kipoi.get_model("/home/mheinzinger/tmp/models/SeqVec/embedding2structure")
def __init__(self, acc_model, don_model, features_path=None):
self.don_model = joblib.load(don_model)
self.acc_model = joblib.load(acc_model)
if features_path is None:
features_path = os.path.join(this_dir, "../features.json")
self.features_metadata = read_json(features_path)
# acceptor and donor site indexes are unified across SOI
# NB! This indexes are pos=1 of the region, and index-1 is already pos=-1, not 0!
self.don_i = 3
self.acc_i = -21
self.labranchor = kipoi.get_model("labranchor", with_dataloader=False)
# add current dir to python path for multiprocessing
sys.path.append(this_dir)
def __init__(self, x=1):
#self.embed = kipoi.get_model("SeqVec/embedding")
#self.struct = kipoi.get_model("SeqVec/embedding2structure")
self.embed = kipoi.get_model("/home/mheinzinger/tmp/models/SeqVec/embedding")
self.struct = kipoi.get_model("/home/mheinzinger/tmp/models/SeqVec/embedding2structure")
def __init__(self):
from keras import backend as K
K.clear_session()
self.model_names = read_txt("models.txt")
# hard-code the path to this models
# if we'd use `source='dir'`, then the models wouldn't
# be updated
self.models = [kipoi.get_model("CpGenie/{0}".format(m), source='kipoi',
with_dataloader=False)
for m in self.model_names]