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-rw-r--r--r_qtl/r_qtl2.py26
1 files changed, 17 insertions, 9 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index f03aff5..1e28bc0 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -368,19 +368,27 @@ def read_geno_file_data(
replace_genotype_codes, genocodes=cdata.get("genotypes", {})))
-def load_geno_samples(zipfilepath: Union[str, Path]) -> tuple[str, ...]:
- """Load the samples/cases/individuals from the 'geno' file(s)."""
+def load_samples(
+ zipfilepath: Union[str, Path], filetype: str) -> tuple[str, ...]:
+ """Load the samples/cases/individuals from file(s) of type 'filetype'."""
cdata = read_control_file(zipfilepath)
- samples = set()
- for genofile in cdata.get("geno", []):
- gdata = read_geno_file_data(zipfilepath, genofile)
- if cdata.get("geno_transposed", False):
- samples.update(next(gdata)[1:])
+ samples: set[str] = set()
+ for afile in cdata.get(filetype, []):
+ filedata = read_geno_file_data(zipfilepath, afile)
+ if cdata.get(f"{filetype}_transposed", False):
+ samples.update(
+ item for item in next(filedata)[1:] if item is not None)
else:
try:
- next(gdata)# Ignore first row.
- samples.update(line[0] for line in gdata)
+ next(filedata)# Ignore first row.
+ samples.update(
+ line[0] for line in filedata if line[0] is not None)
except StopIteration:# Empty file.
pass
return tuple(samples)
+
+
+load_geno_samples = partial(load_samples, filetype="geno")
+load_founder_geno_samples = partial(load_samples, filetype="founder_geno")
+load_pheno_samples = partial(load_samples, filetype="pheno")