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✨ Pass parameters to read #44

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Jan 22, 2025
Merged

✨ Pass parameters to read #44

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -108,3 +108,4 @@ docs/conf.py
_docs_tmp*
*.fcs
*.h5ad
test.ipynb
35 changes: 24 additions & 11 deletions readfcs/_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,21 +247,36 @@ def to_anndata(self, reindex=True) -> ad.AnnData:
for k, v in adata.var.dtypes.items():
if v == "object":
adata.var[k] = adata.var[k].astype("category")

return adata


def read(filepath, reindex=True) -> ad.AnnData:
def read(
filepath: str | Path,
reindex: bool = True,
ignore_offset_error: bool = False,
ignore_offset_discrepancy: bool = False,
use_header_offsets: bool = False,
) -> ad.AnnData:
"""Read in fcs file as AnnData.

Args:
filepath: str or Path
location of fcs file to parse
reindex: bool. Default is True
variables will be reindexed with marker names if possible otherwise channels
filepath: Location of fcs file to parse
reindex: Whether variables will be reindexed with marker names if possible otherwise channels
ignore_offset_error: Ignore data offset error.
ignore_offset_discrepancy: Ignore discrepancy between the HEADER and TEXT values for the DATA byte offset location.
use_header_offsets: Use the HEADER section for the data offset locations.
Setting this option to True also suppresses an error in cases of an offset discrepancy.

Returns:
an AnnData object
An AnnData object
"""
fcsfile = ReadFCS(filepath)
fcsfile = ReadFCS(
filepath,
ignore_offset_error=ignore_offset_error,
ignore_offset_discrepancy=ignore_offset_discrepancy,
use_header_offsets=use_header_offsets,
)
return fcsfile.to_anndata(reindex=reindex)


Expand All @@ -279,13 +294,10 @@ def view(
filepath: Location of fcs file to parse
data_set: Index of retrieved data set in the fcs file.
ignore_offset_error: Ignore data offset error.
Default is False
ignore_offset_discrepancy: Ignore discrepancy between the HEADER and TEXT values for the DATA byte offset location.
Default is False
use_header_offsets: Use the HEADER section for the data offset locations.
Default is False. Setting this option to True also suppresses an error in cases of an offset discrepancy.
Setting this option to True also suppresses an error in cases of an offset discrepancy.
only_text: Only read the “text” segment of the FCS file without loading event data.
Default is False

Returns:
a tuple of (data, metadata)
Expand All @@ -310,4 +322,5 @@ def view(

# meta
meta = flow_data.text

return meta, data
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