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Release 1.35.0 #363

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merged 3 commits into from
Aug 26, 2024
Merged

Release 1.35.0 #363

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d6264a8
Adding h5ad expression type for DE analysis
bistline Aug 26, 2024
3ea1d42
adding reference output file, updating tests
bistline Aug 26, 2024
858bb96
Merge pull request #362 from broadinstitute/jb-h5ad-de
bistline Aug 26, 2024
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2 changes: 1 addition & 1 deletion ingest/cli_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@


# Ingest file types
EXPRESSION_FILE_TYPES = ["dense", "mtx", "loom"]
EXPRESSION_FILE_TYPES = ["dense", "mtx", "h5ad"]


def bq_dataset_exists(dataset):
Expand Down
17 changes: 12 additions & 5 deletions ingest/de.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,8 +197,8 @@ def execute_de(self):
self.genes_path,
self.barcodes_path,
)
elif self.matrix_file_type == "dense":
DifferentialExpression.de_logger.info("preparing DE on dense matrix")
elif self.matrix_file_type == "dense" or self.matrix_file_type == "h5ad":
DifferentialExpression.de_logger.info(f"preparing DE on {self.matrix_file_type} matrix")
self.run_scanpy_de(
self.cluster,
self.metadata,
Expand All @@ -211,7 +211,7 @@ def execute_de(self):
self.method,
)
else:
msg = f"Submitted matrix_file_type should be \"dense\" or \"mtx\" not \"{self.matrix_file_type}\""
msg = f"Submitted matrix_file_type should be \"dense\", \"mtx\" or \"h5ad\" not \"{self.matrix_file_type}\""
print(msg)
log_exception(
DifferentialExpression.dev_logger,
Expand Down Expand Up @@ -337,14 +337,21 @@ def run_scanpy_de(
matrix_object = IngestFiles(matrix_file_path, None)
local_file_path = matrix_object.resolve_path(matrix_file_path)[1]
adata = sc.read(local_file_path)
elif matrix_file_type == "h5ad":
matrix_object = IngestFiles(matrix_file_path, None)
local_file_path = matrix_object.resolve_path(matrix_file_path)[1]
adata = matrix_object.open_anndata(local_file_path)
else:
# MTX reconstitution UNTESTED (SCP-4203)
# will want try/except here to catch failed data object composition
adata = DifferentialExpression.adata_from_mtx(
matrix_file_path, genes_path, barcodes_path
)

adata = adata.transpose()
if not matrix_file_type == "h5ad":
adata = adata.transpose()

use_raw = True if matrix_file_type == "h5ad" else False

adata = DifferentialExpression.subset_adata(adata, de_cells)

Expand All @@ -362,7 +369,7 @@ def run_scanpy_de(
adata,
annotation,
key_added=rank_key,
use_raw=False,
use_raw=use_raw,
method=method,
pts=True,
)
Expand Down
4 changes: 4 additions & 0 deletions ingest/ingest_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,10 @@

# Differential expression analysis (sparse matrix)
python ingest_pipeline.py --study-id addedfeed000000000000000 --study-file-id dec0dedfeed1111111111111 differential_expression --annotation-name cell_type__ontology_label --annotation-type group --annotation-scope study --matrix-file-path ../tests/data/differential_expression/sparse/sparsemini_matrix.mtx --gene-file ../tests/data/differential_expression/sparse/sparsemini_features.tsv --barcode-file ../tests/data/differential_expression/sparse/sparsemini_barcodes.tsv --matrix-file-type mtx --annotation-file ../tests/data/differential_expression/sparse/sparsemini_metadata.txt --cluster-file ../tests/data/differential_expression/sparse/sparsemini_cluster.txt --cluster-name de_sparse_integration --study-accession SCPsparsemini --differential-expression

# Differential expression analysis (h5ad matrix)
python ingest_pipeline.py --study-id addedfeed000000000000000 --study-file-id dec0dedfeed1111111111111 differential_expression --annotation-name cell_type__ontology_label --annotation-type group --annotation-scope study --matrix-file-path ../tests/data/differential_expression/de_dense_matrix.tsv --matrix-file-type h5ad --annotation-file ../tests/data/differential_expression/de_dense_metadata.tsv --cluster-file ../tests/data/differential_expression/de_dense_cluster.tsv --cluster-name de_integration --study-accession SCPdev --differential-expression

"""
import json
import logging
Expand Down
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