diff options
Diffstat (limited to 'r_qtl/r_qtl2.py')
| -rw-r--r-- | r_qtl/r_qtl2.py | 26 |
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") |