scdataloader 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

scdataloader/utils.py

@@ -11,9 +11,14 @@ from django.db import IntegrityError
 from scipy.sparse import csr_matrix
 from scipy.stats import median_abs_deviation
 from functools import lru_cache
+from collections import Counter
 
+from typing import Union, List, Optional
 
-def createFoldersFor(filepath):
+from anndata import AnnData
+
+
+def createFoldersFor(filepath: str):
     """
     will recursively create folders if needed until having all the folders required to save the file in this filepath
     """
@@ -24,7 +29,9 @@ def createFoldersFor(filepath):
             os.mkdir(prevval)
 
 
-def _fetchFromServer(ensemble_server, attributes):
+def _fetchFromServer(
+    ensemble_server: str, attributes: list, database: str = "hsapiens_gene_ensembl"
+):
     """
     Fetches data from the specified ensemble server.
 
@@ -36,7 +43,7 @@ def _fetchFromServer(ensemble_server, attributes):
         pd.DataFrame: A pandas DataFrame containing the fetched data.
     """
     server = BiomartServer(ensemble_server)
-    ensmbl = server.datasets["hsapiens_gene_ensembl"]
+    ensmbl = server.datasets[database]
     print(attributes)
     res = pd.read_csv(
         io.StringIO(
@@ -48,11 +55,12 @@ def _fetchFromServer(ensemble_server, attributes):
 
 
 def getBiomartTable(
-    ensemble_server="http://jul2023.archive.ensembl.org/biomart",
-    useCache=False,
-    cache_folder="/tmp/biomart/",
-    attributes=[],
-    bypass_attributes=False,
+    ensemble_server: str = "http://jul2023.archive.ensembl.org/biomart",
+    useCache: bool = False,
+    cache_folder: str = "/tmp/biomart/",
+    attributes: List[str] = [],
+    bypass_attributes: bool = False,
+    database: str = "hsapiens_gene_ensembl",
 ):
     """generate a genelist dataframe from ensembl's biomart
 
@@ -88,7 +96,7 @@ def getBiomartTable(
     else:
         print("downloading gene names from biomart")
 
-        res = _fetchFromServer(ensemble_server, attr + attributes)
+        res = _fetchFromServer(ensemble_server, attr + attributes, database=database)
         res.to_csv(cachefile, index=False)
 
     res.columns = attr + attributes
@@ -102,7 +110,7 @@ def getBiomartTable(
     return res
 
 
-def validate(adata, organism):
+def validate(adata: AnnData, organism: str):
     """
     validate checks if the adata object is valid for lamindb
 
@@ -144,9 +152,6 @@ def validate(adata, organism):
             raise ValueError(
                 f"Column '{val}' is missing in the provided anndata object."
             )
-    bionty_source = bt.PublicSource.filter(
-        entity="DevelopmentalStage", organism=organism
-    ).one()
 
     if not bt.Ethnicity.validate(
         adata.obs["self_reported_ethnicity_ontology_term_id"],
@@ -169,14 +174,10 @@ def validate(adata, organism):
         adata.obs["cell_type_ontology_term_id"], field="ontology_id"
     ).all():
         raise ValueError("Invalid cell type ontology term id found")
-    if (
-        not bt.DevelopmentalStage.filter(bionty_source=bionty_source)
-        .validate(
-            adata.obs["development_stage_ontology_term_id"],
-            field="ontology_id",
-        )
-        .all()
-    ):
+    if not bt.DevelopmentalStage.validate(
+        adata.obs["development_stage_ontology_term_id"],
+        field="ontology_id",
+    ).all():
         raise ValueError("Invalid dev stage ontology term id found")
     if not bt.Tissue.validate(
         adata.obs["tissue_ontology_term_id"], field="ontology_id"
@@ -186,18 +187,16 @@ def validate(adata, organism):
         adata.obs["assay_ontology_term_id"], field="ontology_id"
     ).all():
         raise ValueError("Invalid assay ontology term id found")
-    if (
-        not bt.Gene.filter(organism=bt.settings.organism)
-        .validate(adata.var.index, field="ensembl_gene_id")
-        .all()
-    ):
+    if not bt.Gene.validate(
+        adata.var.index, field="ensembl_gene_id", organism=organism
+    ).all():
         raise ValueError("Invalid gene ensembl id found")
     return True
 
 
 # setting a cache of 200 elements
 # @lru_cache(maxsize=200)
-def get_all_ancestors(val, df):
+def get_all_ancestors(val: str, df: pd.DataFrame):
     if val not in df.index:
         return set()
     parents = df.loc[val].parents__ontology_id
@@ -207,7 +206,7 @@ def get_all_ancestors(val, df):
         return set.union(set(parents), *[get_all_ancestors(val, df) for val in parents])
 
 
-def get_ancestry_mapping(all_elem, onto_df):
+def get_ancestry_mapping(all_elem: list, onto_df: pd.DataFrame):
     """
     This function generates a mapping of all elements to their ancestors in the ontology dataframe.
 
@@ -242,12 +241,12 @@ def get_ancestry_mapping(all_elem, onto_df):
 
 
 def load_dataset_local(
-    remote_dataset,
-    download_folder,
-    name,
-    description,
-    use_cache=True,
-    only=None,
+    remote_dataset: ln.Collection,
+    download_folder: str,
+    name: str,
+    description: str,
+    use_cache: bool = True,
+    only: Optional[List[int]] = None,
 ):
     """
     This function loads a remote lamindb dataset to local.
@@ -303,7 +302,7 @@ def load_dataset_local(
     return dataset
 
 
-def load_genes(organisms):
+def load_genes(organisms: Union[str, list] = "NCBITaxon:9606"):  # "NCBITaxon:10090",
     organismdf = []
     if type(organisms) == str:
         organisms = [organisms]
@@ -313,7 +312,7 @@ def load_genes(organisms):
         ).df()
         genesdf = genesdf[~genesdf["public_source_id"].isna()]
         genesdf = genesdf.drop_duplicates(subset="ensembl_gene_id")
-        genesdf = genesdf.set_index("ensembl_gene_id")
+        genesdf = genesdf.set_index("ensembl_gene_id").sort_index()
         # mitochondrial genes
         genesdf["mt"] = genesdf.symbol.astype(str).str.startswith("MT-")
         # ribosomal genes
@@ -326,14 +325,14 @@ def load_genes(organisms):
 
 
 def populate_my_ontology(
-    organisms=["NCBITaxon:10090", "NCBITaxon:9606"],
-    sex=["PATO:0000384", "PATO:0000383"],
-    celltypes=[],
-    ethnicities=[],
-    assays=[],
-    tissues=[],
-    diseases=[],
-    dev_stages=[],
+    organisms: List[str] = ["NCBITaxon:10090", "NCBITaxon:9606"],
+    sex: List[str] = ["PATO:0000384", "PATO:0000383"],
+    celltypes: List[str] = [],
+    ethnicities: List[str] = [],
+    assays: List[str] = [],
+    tissues: List[str] = [],
+    diseases: List[str] = [],
+    dev_stages: List[str] = [],
 ):
     """
     creates a local version of the lamin ontologies and add the required missing values in base ontologies
@@ -360,20 +359,20 @@ def populate_my_ontology(
         dev_stages (list, optional): List of developmental stages. Defaults to [].
     """
 
-    names = bt.CellType.from_public().df().index if not celltypes else celltypes
+    names = bt.CellType.public().df().index if not celltypes else celltypes
     records = bt.CellType.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(celltypes))
     bt.CellType(name="unknown", ontology_id="unknown").save()
     # Organism
-    names = bt.Organism.from_public().df().index if not organisms else organisms
+    names = bt.Organism.public().df().index if not organisms else organisms
     records = [
         i[0] if type(i) is list else i
         for i in [bt.Organism.from_public(ontology_id=i) for i in names]
     ]
-    ln.save(records)
+    ln.save(records, parents=bool(organisms))
     bt.Organism(name="unknown", ontology_id="unknown").save()
     # Phenotype
-    names = bt.Phenotype.from_public().df().index if not sex else sex
+    names = bt.Phenotype.public().df().index if not sex else sex
     records = [
         bt.Phenotype.from_public(
             ontology_id=i,
@@ -383,38 +382,49 @@ def populate_my_ontology(
         )
         for i in names
     ]
-    ln.save(records)
+    ln.save(records, parents=bool(sex))
     bt.Phenotype(name="unknown", ontology_id="unknown").save()
     # ethnicity
-    names = bt.Ethnicity.from_public().df().index if not ethnicities else ethnicities
+    names = bt.Ethnicity.public().df().index if not ethnicities else ethnicities
     records = bt.Ethnicity.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(ethnicities))
     bt.Ethnicity(
         name="unknown", ontology_id="unknown"
     ).save()  # multi ethnic will have to get renamed
     # ExperimentalFactor
-    names = bt.ExperimentalFactor.from_public().df().index if not assays else assays
+    names = bt.ExperimentalFactor.public().df().index if not assays else assays
     records = bt.ExperimentalFactor.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(assays))
     bt.ExperimentalFactor(name="unknown", ontology_id="unknown").save()
     # lookup = bt.ExperimentalFactor.lookup()
     # lookup.smart_seq_v4.parents.add(lookup.smart_like)
     # Tissue
-    names = bt.Tissue.from_public().df().index if not tissues else tissues
+    names = bt.Tissue.public().df().index if not tissues else tissues
     records = bt.Tissue.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(tissues))
     bt.Tissue(name="unknown", ontology_id="unknown").save()
     # DevelopmentalStage
     names = (
-        bt.DevelopmentalStage.from_public().df().index if not dev_stages else dev_stages
+        bt.DevelopmentalStage.public().df().index if not dev_stages else dev_stages
     )
     records = bt.DevelopmentalStage.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(dev_stages))
     bt.DevelopmentalStage(name="unknown", ontology_id="unknown").save()
+
+    names = bt.DevelopmentalStage.public(organism="mouse").df().name
+    bionty_source = bt.PublicSource.filter(
+        entity="DevelopmentalStage", organism="mouse"
+    ).one()
+    records = [
+        bt.DevelopmentalStage.from_public(name=i, public_source=bionty_source)
+        for i in names.tolist()
+    ]
+    records[-4] = records[-4][0]
+    ln.save(records)
     # Disease
-    names = bt.Disease.from_public().df().index if not diseases else diseases
+    names = bt.Disease.public().df().index if not diseases else diseases
     records = bt.Disease.from_values(names, field="ontology_id")
-    ln.save(records)
+    ln.save(records, parents=bool(diseases))
     bt.Disease(name="normal", ontology_id="PATO:0000461").save()
     bt.Disease(name="unknown", ontology_id="unknown").save()
     # genes
@@ -430,7 +440,7 @@ def populate_my_ontology(
         ln.save(records)
 
 
-def is_outlier(adata, metric: str, nmads: int):
+def is_outlier(adata: AnnData, metric: str, nmads: int):
     """
     is_outlier detects outliers in adata.obs[metric]
 
@@ -449,7 +459,7 @@ def is_outlier(adata, metric: str, nmads: int):
     return outlier
 
 
-def length_normalize(adata, gene_lengths):
+def length_normalize(adata: AnnData, gene_lengths: list):
     """
     length_normalize normalizes the counts by the gene length
 
@@ -464,7 +474,7 @@ def length_normalize(adata, gene_lengths):
     return adata
 
 
-def pd_load_cached(url, loc="/tmp/", cache=True, **kwargs):
+def pd_load_cached(url: str, loc: str = "/tmp/", cache: bool = True, **kwargs):
     """
     pd_load_cached downloads a file from a url and loads it as a pandas dataframe
 
@@ -482,3 +492,36 @@ def pd_load_cached(url, loc="/tmp/", cache=True, **kwargs):
         urllib.request.urlretrieve(url, loc)
     # Load the data from the file
     return pd.read_csv(loc, **kwargs)
+
+
+def translate(
+    val: Union[str, list, set, Counter, dict], t: str = "cell_type_ontology_term_id"
+):
+    """
+    translate translates the ontology term id to the name
+
+    Args:
+        val (str, dict, set, list, dict): the object to translate
+        t (flat, optional): the type of ontology terms.
+            one of cell_type_ontology_term_id, assay_ontology_term_id, tissue_ontology_term_id.
+            Defaults to "cell_type_ontology_term_id".
+
+    Returns:
+        dict: the mapping for the translation
+    """
+    if t == "cell_type_ontology_term_id":
+        obj = bt.CellType.public(organism="all")
+    elif t == "assay_ontology_term_id":
+        obj = bt.ExperimentalFactor.public()
+    elif t == "tissue_ontology_term_id":
+        obj = bt.Tissue.public()
+    else:
+        return None
+    if type(val) is str:
+        return {val: obj.search(val, field=obj.ontology_id).name.iloc[0]}
+    elif type(val) is list or type(val) is set:
+        return {i: obj.search(i, field=obj.ontology_id).name.iloc[0] for i in set(val)}
+    elif type(val) is dict or type(val) is Counter:
+        return {
+            obj.search(k, field=obj.ontology_id).name.iloc[0]: v for k, v in val.items()
+        }

{scdataloader-0.0.3.dist-info → scdataloader-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scdataloader
-Version: 0.0.3
+Version: 0.0.4
 Summary: a dataloader for single cell data in lamindb
 Home-page: https://github.com/jkobject/scDataLoader
 License: GPL3
@@ -34,6 +34,8 @@ Description-Content-Type: text/markdown
 
 [![codecov](https://codecov.io/gh/jkobject/scDataLoader/branch/main/graph/badge.svg?token=scDataLoader_token_here)](https://codecov.io/gh/jkobject/scDataLoader)
 [![CI](https://github.com/jkobject/scDataLoader/actions/workflows/main.yml/badge.svg)](https://github.com/jkobject/scDataLoader/actions/workflows/main.yml)
+[![DOI](https://zenodo.org/badge/731248665.svg)](https://zenodo.org/doi/10.5281/zenodo.10573143)
+
 
 Awesome single cell dataloader created by @jkobject 
 
@@ -66,7 +68,7 @@ the idea is to use it to train models like scGPT / GeneFormer (and soon, scPrint
 
 Currently one would have to use the preprocess function to make the dataset fit for different tools like scGPT / Geneformer. But I would want to enable it through different Collators. This is still missing and a WIP... (please do contribute!)
 
-![](docs/scdataloader.drawio.png)
+![docs/scdataloader.drawio.png](docs/scdataloader.drawio.png)
 
 ## Install it from PyPI
 
@@ -85,6 +87,48 @@ then run the notebooks with the poetry installed environment
 
 ## Usage
 
+```python
+# initialize a local lamin database
+# !lamin init --storage ~/scdataloader --schema bionty
+
+from scdataloader import utils
+from scdataloader.preprocess import LaminPreprocessor, additional_postprocess, additional_preprocess
+
+# preprocess datasets
+DESCRIPTION='preprocessed by scDataLoader'
+
+cx_dataset = ln.Collection.using(instance="laminlabs/cellxgene").filter(name="cellxgene-census", version='2023-12-15').one()
+cx_dataset, len(cx_dataset.artifacts.all())
+
+
+do_preprocess = LaminPreprocessor(additional_postprocess=additional_postprocess, additional_preprocess=additional_preprocess, skip_validate=True, subset_hvg=0)
+
+preprocessed_dataset = do_preprocess(cx_dataset, name=DESCRIPTION, description=DESCRIPTION, start_at=6, version="2")
+
+# create dataloaders
+from scdataloader import DataModule
+import tqdm
+
+datamodule = DataModule(
+    collection_name="preprocessed dataset",
+    organisms=["NCBITaxon:9606"], #organism that we will work on
+    how="most expr", # for the collator (most expr genes only will be selected)
+    max_len=1000, # only the 1000 most expressed
+    batch_size=64,
+    num_workers=1,
+    validation_split=0.1,
+    test_split=0)
+
+for i in tqdm.tqdm(datamodule.train_dataloader()):
+    # pass #or do pass
+    print(i)
+    break
+
+# with lightning:
+# Trainer(model, datamodule)
+
+```
+
 see the notebooks in [docs](https://jkobject.github.io/scDataLoader/):
 
 1. [load a dataset](https://jkobject.github.io/scDataLoader/notebooks/01_load_dataset.html)

scdataloader-0.0.4.dist-info/RECORD

@@ -0,0 +1,16 @@
+scdataloader/VERSION,sha256=ln2a-xATRmZxZvLnboGRC8GQSI19QdUMoAcunZLwDjI,6
+scdataloader/__init__.py,sha256=NIlE4oTUPRZ3uSW_maozoEHp470I7PV1vMOJ4XpSmL4,122
+scdataloader/__main__.py,sha256=UyXtFHgWxE-ecJmM_oEDLlzBDBbH-uEKAVj1A7BkwmM,6297
+scdataloader/base.py,sha256=M1gD59OffRdLOgS1vHKygOomUoAMuzjpRtAfM3SBKF8,338
+scdataloader/collator.py,sha256=Ykjdw24GUvHdbowWUDtp28YTkaF3w65SiWTU2PKBzy4,11714
+scdataloader/config.py,sha256=0_LoIblgdZZ19yM2qvPE-padMGQzdhuaxX20zYrhWq0,2780
+scdataloader/data.py,sha256=faJWN--06N7irWBKcjeU6fcX5NbzyEPXs2_EVGxfBpw,12292
+scdataloader/datamodule.py,sha256=OhHPb3jhGG5HbvahzTGxgzJ_lxbVJ4PfZspVW9h7SZk,14789
+scdataloader/mapped.py,sha256=rhE11Xl3x_wIKu3m_wu8Is6mYsXdblu3nQpT5lNqr60,13301
+scdataloader/preprocess.py,sha256=67ewe6b4HIjz_vTDjlOAJ4lMe4K2oCw2HHHUS-7S77M,38205
+scdataloader/utils.py,sha256=6eKU3_cotEaQcxONMrCWzMx7U8DybabteNhk-vNqfUQ,19365
+scdataloader-0.0.4.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+scdataloader-0.0.4.dist-info/METADATA,sha256=Bf8UjMwRcqSbWW8VbWrLhSb7qKQYdjZtJ7d6Oz4-rn8,39733
+scdataloader-0.0.4.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+scdataloader-0.0.4.dist-info/entry_points.txt,sha256=nLqucZaa5wiF7-1FCgMXO916WDQ9Qm0TcxQp0f1DwE4,59
+scdataloader-0.0.4.dist-info/RECORD,,