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February 10, 2019 11:00
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Add a "tracker" attribute to AnnData objects to keep track of transformations to it's data
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import scanpy.api as sc | |
import numpy as np | |
def add_tracker(field_name="tracker"): | |
from inspect import getcallargs | |
from functools import wraps | |
def tracker(f): | |
@wraps(f) | |
def wrapper(*args, **kwds): | |
adata = args[0] | |
if field_name not in adata.uns: | |
adata.uns[field_name] = np.array([], dtype="<U32") | |
adata.uns[field_name] = np.append(adata.uns[field_name], [f.__name__]) | |
return f(*args, **kwds) | |
return wrapper | |
pp_functions = filter( | |
lambda x: list(getcallargs(getattr(sc.pp, x), None, None).keys())[0] in ["adata", "data"], | |
filter( | |
lambda x: not x.startswith("__"), sc.pp.__dict__.keys())) | |
for function in pp_functions: | |
setattr(sc.pp, function, tracker(getattr(sc.pp, function))) | |
add_tracker() | |
a = sc.AnnData(np.random.randint(0, 100, size=(20, 5))) | |
assert "tracker" not in a.uns | |
sc.pp.normalize_per_cell(a) | |
assert "tracker" in a.uns | |
assert a.uns['tracker'] == np.array(["normalize_per_cell"]) | |
sc.pp.log1p(a) | |
assert all(a.uns['tracker'] == np.array(["normalize_per_cell", "log1p"])) | |
sc.write("example_anndata.h5ad", a) | |
a = sc.read("example_anndata.h5ad") | |
assert "tracker" in a.uns | |
assert all(a.uns['tracker'] == np.array(["normalize_per_cell", "log1p"])) |
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I'd prefer to have a ,more simple and discrete class attribute e.g. "_tracker" of type
list
to track, but since saving as h5ad is not true object serialization, adding it touns
seemed like the other obvious way.