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| author | Frederick Muriuki Muriithi | 2024-01-15 17:49:14 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-15 17:49:14 +0300 |
| commit | 42b43f8d46fe0c25703de914a687127726ece35e (patch) | |
| tree | f30490a689be720969a1a57cd3bd92e9abf68739 /r_qtl | |
| parent | ef6da7313f96390b9fecb126f9b7e9beb1afe034 (diff) | |
| download | gn-uploader-42b43f8d46fe0c25703de914a687127726ece35e.tar.gz | |
Extract common functional tools to separate package.
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/r_qtl2.py | 18 |
1 files changed, 7 insertions, 11 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index b2a7acf..b688404 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -8,14 +8,10 @@ from typing import Iterator, Iterable, Callable import yaml -from quality_control.parsing import take +from functional_tools import take, chain from r_qtl.errors import InvalidFormat -def thread_op(value, *functions): - """Thread the `value` through the sequence of `functions`.""" - return reduce(lambda result, func: func(result), functions, value) - def control_data(zfile: ZipFile) -> dict: """Retrieve the control file from the zip file info.""" files = tuple(filename @@ -140,7 +136,7 @@ def make_process_data_geno(cdata) -> tuple[ return val def __non_transposed__(row: dict) -> dict: return { - key: thread_op(value, replace_genotype_codes, replace_na_strings) + key: chain(value, replace_genotype_codes, replace_na_strings) for key,value in row.items() } def __transposed__(id_key: str, @@ -149,7 +145,7 @@ def make_process_data_geno(cdata) -> tuple[ return tuple( dict(zip( [id_key, vals[0]], - (thread_op(item, replace_genotype_codes, replace_na_strings) + (chain(item, replace_genotype_codes, replace_na_strings) for item in items))) for items in zip(ids, vals[1:])) return (__non_transposed__, __transposed__) @@ -179,7 +175,7 @@ def make_process_data_covar(cdata) -> tuple[ rep_cross_info = partial(replace_cross_info, cdata=cdata) def non_transposed(row: dict) -> dict: return { - key: thread_op(value, rep_sex_info, rep_cross_info) + key: chain(value, rep_sex_info, rep_cross_info) for key,value in row.items() } def transposed(id_key: str, @@ -188,7 +184,7 @@ def make_process_data_covar(cdata) -> tuple[ return tuple( dict(zip( [id_key, vals[0]], - (thread_op(item, rep_sex_info, rep_cross_info) + (chain(item, rep_sex_info, rep_cross_info) for item in items))) for items in zip(ids, vals[1:])) return (non_transposed, transposed) @@ -245,7 +241,7 @@ def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: new_cdata, *make_process_data_covar(cdata)): yield { - key: thread_op(value, partial(replace_cross_info, cdata=cdata)) + key: chain(value, partial(replace_cross_info, cdata=cdata)) for key, value in row.items() if key not in sex_fields} def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: @@ -263,7 +259,7 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: new_cdata, *make_process_data_covar(cdata)): yield { - key: thread_op(value, partial(replace_sex_info, cdata=cdata)) + key: chain(value, partial(replace_sex_info, cdata=cdata)) for key, value in row.items() if key not in ci_fields} def validate_bundle(zfile: ZipFile): |