def get(self, dataset_id):
analysis_id = request.args.get('analysis')
session_id = request.cookies.get('gear_session_id')
user = geardb.get_user_from_session_id(session_id)
if analysis_id:
ana = geardb.Analysis(id=analysis_id,
dataset_id=dataset_id,
session_id=session_id,
user_id=user.id)
ana.discover_type()
adata = sc.read_h5ad(ana.dataset_path())
else:
ds = geardb.Dataset(id=dataset_id, has_h5ad=1)
h5_path = ds.get_file_path()
# Let's not fail if the file isn't there
if not os.path.exists(h5_path):
return {
"success": -1,
"message": "No h5 file found for this dataset"
}
adata = sc.read_h5ad(h5_path)
return {"success": 1, "gene_symbols": adata.var.gene_symbol.tolist()}
def test_fixup_gene_symbols_seurat(self):
if not os.path.isfile(self.seurat_path):
return unittest.skip(
"Skipping gene symbol conversion tests because test h5ads are not present. To create them, "
"run local_server/test/fixtures/schema_test_data/generate_test_data.sh"
)
original_adata = sc.read_h5ad(self.seurat_path)
merged_adata = sc.read_h5ad(self.seurat_merged_path)
fixup_config = {"X": "log1p", "counts": "raw", "scale.data": "log1p"}
fixed_adata = remix.fixup_gene_symbols(original_adata, fixup_config)
self.assertEqual(
merged_adata.layers["counts"][:, merged_adata.var.index == self.stable_gene].sum(),
fixed_adata.raw.X[:, fixed_adata.var.index == self.stable_gene].sum()
)
self.assertAlmostEqual(
merged_adata.X[:, merged_adata.var.index == self.stable_gene].sum(),
fixed_adata.X[:, fixed_adata.var.index == self.stable_gene].sum()
)
self.assertAlmostEqual(
merged_adata.layers["scale.data"][:, merged_adata.var.index == self.stable_gene].sum(),
fixed_adata.layers["scale.data"][:, fixed_adata.var.index == self.stable_gene].sum()
)
def get_train_dataloaders(train, val, batch_size=64, label_col='cell_type'):
"""
Get train and validation dataloaders.
Arguments
---------
train: str or AnnData
- AnnData object or filepath of saved AnnData with .h5ad ext to be used for training
val: str or AnnData
- AnnData object or filepath of saved AnnData with .h5ad ext to be used for validation
batch_size: int
- batch size for dataloaders
"""
train_adata = sc.read_h5ad(train) if isinstance(train, str) else train
val_adata = sc.read_h5ad(val) if isinstance(val, str) else val
train_adata = normalize(train_adata)
val_adata = normalize(val_adata, var_order=train_adata.var.index.to_list())
train_ds = PollockDataset(train_adata, label_col=label_col)
val_ds = PollockDataset(val_adata, label_col=label_col)
train_dl = DataLoader(train_ds, batch_size=batch_size, shuffle=True)
val_dl = DataLoader(val_ds, batch_size=batch_size, shuffle=False)
return train_dl, val_dl
def test_fixup_gene_symbols_sctransform(self):
if not os.path.isfile(self.sctransform_path):
return unittest.skip(
"Skipping gene symbol conversion tests because test h5ads are not present. To create them, "
"run local_server/test/fixtures/schema_test_data/generate_test_data.sh"
)
original_adata = sc.read_h5ad(self.sctransform_path)
merged_adata = sc.read_h5ad(self.sctransform_merged_path)
fixup_config = {"X": "log1p", "counts": "raw"}
fixed_adata = remix.fixup_gene_symbols(original_adata, fixup_config)
# sctransform does a bunch of stuff, including slightly modifying the
# raw counts. So we can't assert for exact equality the way we do with
# the vanilla seurat tutorial. But, the results should still be very
# close.
merged_raw_stable = merged_adata.layers["counts"][:, merged_adata.var.index == self.stable_gene].sum()
fixed_raw_stable = fixed_adata.raw.X[:, fixed_adata.var.index == self.stable_gene].sum()
self.assertLess(abs(merged_raw_stable - fixed_raw_stable), .001 * merged_raw_stable)
self.assertAlmostEqual(
merged_adata.X[:, merged_adata.var.index == self.stable_gene].sum(),
fixed_adata.X[:, fixed_adata.var.index == self.stable_gene].sum(),
0
)
def load_file(path):
"""
Load single cell dataset from file
Parameters
----------
path
the path store the file
Return
------
AnnData
"""
if os.path.exists(DATA_PATH + path + '.h5ad'):
adata = sc.read_h5ad(DATA_PATH + path + '.h5ad')
elif os.path.isdir(path): # mtx format
adata = read_mtx(path)
elif os.path.isfile(path):
if path.endswith(('.csv', '.csv.gz')):
adata = sc.read_csv(path).T
elif path.endswith(('.txt', '.txt.gz', '.tsv', '.tsv.gz')):
df = pd.read_csv(path, sep='\t', index_col=0).T
adata = AnnData(df.values, dict(obs_names=df.index.values),
dict(var_names=df.columns.values))
elif path.endswith('.h5ad'):
adata = sc.read_h5ad(path)
else:
raise ValueError("File {} not exists".format(path))
if not issparse(adata.X):
adata.X = scipy.sparse.csr_matrix(adata.X)
adata.var_names_make_unique()
return adata
def load_PB_datasets(path='data'):
#Import datasets
'/'.join([path, 'droplet_pseudobulk.h5ad'])
droplet = scanpy.read_h5ad('/'.join([path, 'droplet_pseudobulk.h5ad']))
facs = scanpy.read_h5ad('/'.join([path, 'facs_pseudobulk.h5ad']))
mca = scanpy.read_h5ad('/'.join([path, 'mca_pseudobulk.h5ad']))
return droplet, facs, mca
def test_read_10x(tmp_path, mtx_path, h5_path, prefix):
if prefix is not None:
# Build files named "prefix_XXX.xxx" in a temporary directory.
mtx_path_orig = mtx_path
mtx_path = tmp_path / "filtered_gene_bc_matrices_prefix"
mtx_path.mkdir()
for item in mtx_path_orig.iterdir():
if item.is_file():
shutil.copyfile(item, mtx_path / f"{prefix}{item.name}")
mtx = sc.read_10x_mtx(mtx_path, var_names="gene_symbols", prefix=prefix)
h5 = sc.read_10x_h5(h5_path)
# Drop genome column for comparing v3
if "3.0.0" in str(h5_path):
h5.var.drop(columns="genome", inplace=True)
# Check equivalence
assert_anndata_equal(mtx, h5)
# Test that it can be written:
from_mtx_pth = tmp_path / "from_mtx.h5ad"
from_h5_pth = tmp_path / "from_h5.h5ad"
mtx.write(from_mtx_pth)
h5.write(from_h5_pth)
assert_anndata_equal(sc.read_h5ad(from_mtx_pth), sc.read_h5ad(from_h5_pth))
def read_species(human=True):
""" Returns either the human or mouse anndata object
human = True if you want the human object, false will give you the mouse object
"""
if human == True:
return (sc.read_h5ad("DataBySpecies/human.anndata.h5ad"))
else:
return (sc.read_h5ad("DataBySpecies/mouse.anndata.h5ad"))
def test_diversity_rarefaction2(create_testfolder):
f = create_testfolder / "test.h5ad"
adata = sc.read_h5ad(f)
ddl.tl.clone_rarefaction(adata, groupby='sample_id', clone_key='clone_id')
assert 'diversity' in adata.uns
p = ddl.pl.clone_rarefaction(adata, color='sample_id')
assert p is not None
adata = sc.read_h5ad(f)
p = ddl.pl.clone_rarefaction(adata, color='sample_id')
assert p is not None
def __init__(self, original, result):
self.adata = sc.read_h5ad(original, True)
self.adata_out = sc.read_h5ad(result, True)
sum_list = self.adata.obsm["X_umap"][:, 0] - self.adata_out.obsm[
"X_umap_2d"][:, 0]
diff_sum = 0
for i in sum_list:
diff_sum += i
assert 0.5 > diff_sum > -0.5, "difference too large"
def load_demo_data():
# load the data
stream = pkg_resources.resource_stream(__name__,
'data/RNA_demo_github.h5ad')
rna_data = sc.read_h5ad(stream)
stream = pkg_resources.resource_stream(__name__,
'data/ACC_demo_github.h5ad')
acc_data = sc.read_h5ad(stream)
stream = pkg_resources.resource_stream(__name__,
'data/GLUER_demo_github.h5ad')
gluer_data = sc.read_h5ad(stream)
return rna_data, acc_data, gluer_data
def load_data(data_name, data_dir=None, dtype=float, load_metadata=True):
import scanpy as sc
import pandas as pd
metadata = None
if data_name.lower() == 'mnist':
if data_dir is None:
data_dir = "./data/"
data_path = os.path.join(data_dir, "mnist2500_X.txt")
X = np.loadtxt(data_path).astype(dtype)
if load_metadata:
metadata_path = os.path.join(data_dir, "mnist2500_labels.txt")
metadata = np.loadtxt(metadata_path).astype(int)
metadata = pd.DataFrame(metadata, columns=['label'])
elif data_name.lower() in tabula_muris_tissues:
if data_dir is None:
data_dir = "./data/tabula-muris/04_facs_processed_data/FACS/"
data_file = f"Processed_{data_name.title()}.h5ad"
data_path = os.path.join(data_dir, data_file)
X = sc.read_h5ad(data_path)
metadata = X.obs.copy()
X = X.obsm['X_pca']
elif data_name.lower() == "ATAC":
if data_dir is None:
data_dir = "./data/10kPBMC_scATAC/02_processed_data/"
data_file = f"atac_pbmc_10k_nextgem_preprocessed_data.h5ad"
data_path = os.path.join(data_dir, data_file)
X = sc.read_h5ad(data_path)
metadata = X.obs.copy()
X = X.obsm['lsi']
if load_metadata:
return X, metadata
else:
return X
def get(self, dataset_id):
args = request.args
analysis_id = args.get('analysis_id')
session_id = request.cookies.get('gear_session_id')
if analysis_id:
# session_id = request.cookies.get('gear_session_id')
user = geardb.get_user_from_session_id(session_id)
ana = geardb.Analysis(id=analysis_id, dataset_id=dataset_id, session_id=session_id, user_id=user.id)
ana.discover_type()
adata = sc.read_h5ad(ana.dataset_path())
else:
ds = geardb.Dataset(id=dataset_id, has_h5ad=1)
h5_path = ds.get_file_path()
# Let's not fail if the file isn't there
if not os.path.exists(h5_path):
return {
"success": -1,
"message": "No h5 file found for this dataset"
}
adata = sc.read_h5ad(h5_path)
columns = adata.obs.columns.tolist()
if hasattr(adata, 'obsm') and hasattr(adata.obsm, 'X_tsne'):
columns.append('X_tsne_1')
columns.append('X_tsne_2')
if 'replicate' in columns:
columns.remove('replicate')
if 'time_point_order' in columns:
columns.remove('time_point_order')
# get a map of all levels for each column
levels = {}
for col in columns:
try:
levels[col] = adata.obs[col].cat.categories.tolist()
except:
pass
# If levels are not categorical I don't believe
# we need to return levels
return {
"success": 1,
"obs_columns": columns,
"obs_levels": levels
}
def oligodendroglioma() -> AnnData:
"""The original inferCNV example dataset.
Derived from :cite:`Tirosh2016`.
"""
with pkg_resources.path(data, "oligodendroglioma.h5ad") as p:
return sc.read_h5ad(p)
def result_export(request):
"""
create a new dataset from selected indexes of observations
"""
pid = request.POST.get("pid", None)
if not pid:
return HttpResponseBadRequest
adata = read_h5ad(
os.path.join(USER_PROCESS_FOLDER, str(pid), "results.h5ad"))
hextime = hex(int(time()))[2:]
output_path = os.path.join(DATASET_FOLDER,
f"exported_{pid}_{hextime}.h5ad")
indexes = np.fromstring(request.POST.get("index"), dtype=int, sep=",")
adata = adata[indexes, :]
adata.write(output_path)
saved_file = DataSet(name=request.POST.get("name", f"export_{pid}"),
path=output_path,
description=request.POST.get("description", ""),
n_obs=adata.n_obs,
n_vars=adata.n_vars,
attrs=json.dumps(get_anndata_attrs(adata)))
saved_file.save()
return JsonResponse({'status': True, 'id': saved_file.id})
def main():
parser = argparse.ArgumentParser(
description='Rename a colum in an H5AD file')
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='Path to an input file to be read')
parser.add_argument('-pre',
'--previous_column',
type=str,
required=True,
help='Name of column which needs changing')
parser.add_argument('-post',
'--post_column',
type=str,
required=True,
help='New name for column')
parser.add_argument('-o',
'--output_file',
type=str,
required=True,
help='Path to an output file to be created')
args = parser.parse_args()
adata = sc.read_h5ad(args.input_file)
adata.obs.rename(columns={args.previous_column: args.post_column},
inplace=True)
adata.write(args.output_file)
def load_h5ad_file(self, input_path, batch_size, datasets=[]):
"""
Load input data from a h5ad file and divide into training and test set
:param input_path: path to h5ad file
:param batch_size: batch size to use for training
:param datasets: a list of datasets to extract from the file
:return: Dataset object
"""
raw_input = sc.read_h5ad(input_path)
# Subset dataset
if len(datasets) > 0:
all_ds = collections.Counter(raw_input.obs['ds'])
for ds in all_ds:
if ds not in datasets:
raw_input = raw_input[raw_input.obs['ds'] != ds].copy()
# Create training dataset
ratios = [raw_input.obs[ctype] for ctype in raw_input.uns['cell_types']]
self.x_data = raw_input.X.astype(np.float32)
self.y_data = np.array(ratios, dtype=np.float32).transpose()
# create placeholders
self.x_data_ph = tf.placeholder(self.x_data.dtype, self.x_data.shape, name="x_data_ph")
self.y_data_ph = tf.placeholder(self.y_data.dtype, self.y_data.shape, name="y_data_ph")
self.data = tf.data.Dataset.from_tensor_slices((self.x_data_ph, self.y_data_ph))
self.data = self.data.shuffle(1000).repeat().batch(batch_size=batch_size)
# Extract celltype and feature info
self.labels = raw_input.uns['cell_types']
self.sig_genes = list(raw_input.var_names)
def _cached_dataset(self):
if self._ignore_cache:
return None
if not self._cache_path.exists():
return None
dataset = sc.read_h5ad(self._cache_path)
return dataset
def test_plot_network(create_testfolder):
f = create_testfolder / "test.h5ad"
adata = sc.read_h5ad(f)
ddl.pl.clone_network(adata,
color=['isotype'],
show=False,
return_fig=False)
def read_10x_data(input_file,
format_type='10x_h5',
backed=None,
transpose=False,
sparse=False):
if format_type == '10x_h5':
adata = sc.read_10x_h5(input_file)
elif format_type == '10x_mtx':
adata = sc.read_10x_mtx(input_file)
elif format_type == '10x_h5ad':
adata = sc.read_h5ad(input_file, backed=backed)
elif format_type == "10x_csv":
adata = sc.read_csv(input_file)
elif format_type == "10x_txt":
adata = sc.read_csv(input_file, delimiter="\t")
else:
raise ValueError('`format` needs to be \'10x_h5\' or \'10x_mtx\'')
if transpose:
adata = adata.transpose()
if sparse:
adata.X = csr_matrix(adata.X, dtype='float32')
adata.var_names_make_unique()
adata.obs_names_make_unique()
return adata
def read_adata(
gex_data, # filename
gex_data_type # string describing file type
):
''' Split this out so that other code can use it. Read GEX data
'''
print('reading:', gex_data, 'of type', gex_data_type)
if gex_data_type == 'h5ad':
adata = sc.read_h5ad( gex_data )
elif gex_data_type == '10x_mtx':
adata = sc.read_10x_mtx( gex_data )
elif gex_data_type == '10x_h5':
adata = sc.read_10x_h5( gex_data, gex_only=True )
elif gex_data_type == 'loom':
adata = sc.read_loom( gex_data )
else:
print('unrecognized gex_data_type:', gex_data_type, "should be one of ['h5ad', '10x_mtx', '10x_h5', 'loom']")
exit()
if adata.isview: # this is so weird
adata = adata.copy()
return adata
def main(ds, strategy):
adata = sc.read_h5ad(ds + '.h5ad')
if adata.raw:
raw_adata = ad.AnnData(adata.raw.X, var=adata.raw.var, obs=adata.obs)
var, to_keep, counts = curate_var(raw_adata.var, strategy)
counts['dataset'] = ds + '-raw'
counts['mapping_file'] = strategy
report(counts)
raw_adata.var = var
raw_adata = raw_adata[:, to_keep]
raw_adata.var.set_index('feature_id', inplace=True)
adata.raw = raw_adata
del raw_adata
gc.collect()
var, to_keep, counts = curate_var(adata.var, strategy)
var['feature_is_filtered'] = False # feature_is_filtered is default False
counts['dataset'] = ds + '-X'
counts['mapping_file'] = strategy
report(counts)
adata.var = var
adata = adata[:, to_keep]
adata.var.set_index('feature_id', inplace=True)
# write the new object to the file
adata.write(filename=ds + '.h5ad', compression='gzip')
del adata
gc.collect()
def get_all_gene(trainset_dir):
dataset_list = os.listdir(trainset_dir)
gene = []
for dataset in dataset_list:
if '.txt' in dataset:
df = pd.read_csv(trainset_dir + dataset, sep='\t')
elif '.csv' in dataset:
df = pd.read_csv(trainset_dir + dataset)
elif '.h5' in dataset and '.h5ad' not in dataset and '_processed' not in dataset:
df = pd.read_hdf(trainset_dir + dataset)
elif '.h5ad' in dataset:
df = sc.read_h5ad(trainset_dir + dataset)
df = df.to_df()
else:
continue
file_gene = df.columns.tolist()
for i in file_gene:
if i == 'cell_label':
continue
if i not in gene:
gene.append(i)
with open('pre_trained/gene/new_model.txt', 'w') as gene_file:
gene_ = ''
for i in gene[:-2]:
gene_ = gene_ + i + ', '
gene_ = gene_ + gene[-2]
gene_ = gene_.lower()
gene_file.write(gene_)
gene = gene_.split(', ')
gene.append('cell_label')
return gene
def preprocess(args):
sc.logging.print_versions()
# # read filtered data from a loom file
# adata = sc.read_loom(args.loom_filtered)
adata = sc.read_h5ad(args.anndata)
# Total-count normalize (library-size correct) to 10,000 reads/cell
sc.pp.normalize_per_cell(adata, counts_per_cell_after=1e4)
# log transform the data.
sc.pp.log1p(adata)
# identify highly variable genes.
sc.pp.highly_variable_genes(adata,
min_mean=0.0125,
max_mean=3,
min_disp=0.5)
sc.pl.highly_variable_genes(adata)
# keep only highly variable genes:
adata = adata[:, adata.var['highly_variable']]
# regress out total counts per cell and the percentage of mitochondrial genes expressed
sc.pp.regress_out(adata, ['n_counts', 'percent_mito'], n_jobs=args.threads)
# scale each gene to unit variance, clip values exceeding SD 10.
sc.pp.scale(adata, max_value=10)
adata.write(args.anndata)
def test_workflow(adata_path, upgrade_schema, obs_expected, tmp_path):
if upgrade_schema:
adata = sc.read_h5ad(adata_path)
ir.io.upgrade_schema(adata)
else:
adata = ir.io.read_10x_vdj(adata_path)
adata_obs_expected = pd.read_pickle(obs_expected)
ir.tl.chain_qc(adata)
ir.pp.ir_dist(adata)
ir.tl.define_clonotypes(adata)
ir.tl.clonotype_network(adata)
ir.tl.clonal_expansion(adata)
ir.pl.clonotype_network(adata)
# test that writing works (i.e. all scirpy fields can be serialized)
adata.write_h5ad(tmp_path / "adata.h5ad")
# turn nans into consistent value (nan)
_normalize_df_types(adata.obs)
# # Use this code to re-generate the "expected file", if necessary.
# adata.obs.to_pickle(obs_expected, protocol=4)
pdt.assert_frame_equal(adata.obs,
adata_obs_expected,
check_dtype=False,
check_categorical=False)
def main():
"""Run CLI."""
parser = argparse.ArgumentParser(description="""
Get a list of all celltypes in an anndataframe.
""")
parser.add_argument('-h5',
'--h5_anndata',
action='store',
dest='h5',
required=True,
help='H5 AnnData file.')
parser.add_argument(
'--cell_label',
action='store',
dest='cell_label',
default='cluster',
help='Anndata cell type label name in obs slot. (default: %(default)s)'
)
options = parser.parse_args()
# Load the AnnData file
adata = sc.read_h5ad(filename=options.h5)
np_array = np.sort(adata.obs[options.cell_label].unique().astype(str))
np.savetxt('cell_labels.csv', np_array, fmt='%s')
def test_apply_bad_schema(self, mock_get_ontology_label):
mock_get_ontology_label.return_value = "test label"
remix.apply_schema(self.source_h5ad_path, self.bad_config_path, self.output_h5ad_path)
new_adata = sc.read_h5ad(self.output_h5ad_path)
# Should refuse to write the version
self.assertNotIn("version", new_adata.uns_keys())
def load_data(data):
if isfile(data):
name, extension = splitext(data)
if extension == ".h5ad":
adata = sc.read_h5ad(data)
elif extension == ".loom":
adata = sc.read_loom(data)
else:
raise click.FileError(data, hint="does not have a valid extension [.h5ad | .loom]")
elif isdir(data):
if not data.endswith(sep):
data += sep
adata = sc.read_10x_mtx(data)
else:
raise click.FileError(data, hint="not a valid file or path")
if not set_obs_names == "":
if set_obs_names not in adata.obs_keys():
raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
adata.obs_names = adata.obs[set_obs_names]
if not set_var_names == "":
if set_var_names not in adata.var_keys():
raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
adata.var_names = adata.var[set_var_names]
if make_obs_names_unique:
adata.obs.index = make_index_unique(adata.obs.index)
if make_var_names_unique:
adata.var.index = make_index_unique(adata.var.index)
if not adata._obs.index.is_unique:
click.echo("Warning: obs index is not unique")
if not adata._var.index.is_unique:
click.echo("Warning: var index is not unique")
return adata
def test_overlap1(create_testfolder):
f = create_testfolder / "test.h5ad"
adata = sc.read_h5ad(f)
ddl.tl.clone_overlap(adata, groupby='group3', colorby='group2')
assert 'clone_overlap' in adata.uns
assert isinstance(adata.uns['clone_overlap'], pd.DataFrame)
ddl.pl.clone_overlap(adata, groupby='group3', colorby='group2')
def render_data(request):
id_ = int(request.GET.get('id', None))
if id_ is None:
return HttpResponseBadRequest
worker = get_object_or_404(WorkerRecord, id=int(id_))
dataset = get_object_or_404(DataSet, name=f"Worker_{id_}")
dataset.attrs = json.loads(dataset.attrs)
path = os.path.join(USER_PROCESS_FOLDER, str(worker.id), 'results.h5ad')
annData = read_h5ad(path)
return render(
request, "process/data.html", {
'worker':
worker,
'vars':
annData.var.reset_index().to_html(
index=False,
classes='mb-0 table table-bordered',
max_rows=10000),
'obs':
annData.obs.reset_index().to_html(
index=False,
classes='mb-0 table table-bordered',
max_rows=10000),
'dataset':
dataset
})
