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-rw-r--r--r_qtl/r_qtl2.py35
1 files changed, 28 insertions, 7 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 02217ee..2c1e162 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -134,6 +134,13 @@ def make_process_data_geno(cdata) -> tuple[
for items in zip(ids, vals[1:]))
return (__non_transposed__, __transposed__)
+def replace_sex_info(val, cdata: dict):
+ """Replace sex information in files with values in the control data."""
+ sex_info = cdata.get("sex", False)
+ if bool(sex_info):
+ return sex_info.get(val, val)
+ return val
+
def replace_cross_info(val, cdata: dict):
"""
Replace cross information in files with the values in the control data.
@@ -148,15 +155,11 @@ def make_process_data_covar(cdata) -> tuple[
Callable[[str, tuple[str, ...], tuple[str, ...]],
tuple[dict, ...]]]:
"""Build functions to process sex and cross information in covar files."""
- def replace_sex_code(val):
- sex_info = cdata.get("sex", False)
- if bool(sex_info):
- return sex_info.get(val, val)
- return val
+ rep_sex_info = partial(replace_sex_info, cdata=cdata)
rep_cross_info = partial(replace_cross_info, cdata=cdata)
def non_transposed(row: dict) -> dict:
return {
- key: thread_op(value, replace_sex_code, rep_cross_info)
+ key: thread_op(value, rep_sex_info, rep_cross_info)
for key,value in row.items()
}
def transposed(id_key: str,
@@ -165,7 +168,7 @@ def make_process_data_covar(cdata) -> tuple[
return tuple(
dict(zip(
[id_key, vals[0]],
- (thread_op(item, replace_sex_code, rep_cross_info)
+ (thread_op(item, rep_sex_info, rep_cross_info)
for item in items)))
for items in zip(ids, vals[1:]))
return (non_transposed, transposed)
@@ -221,3 +224,21 @@ def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
yield {
key: thread_op(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]:
+ """Load cross information where present."""
+ cdata_sex_info = cdata.get("sex", {})
+ sex_info_file_key = "covar"
+ new_cdata = {**cdata}
+ ci_fields = (cdata.get("cross_info",{}).get("covar",""),)
+ if "file" in cdata_sex_info:
+ sex_info_file_key = "gnqc_sex_info_file"
+ new_cdata = {**cdata, "gnqc_sex_info_file": cdata_sex_info["file"]}
+
+ for row in file_data(zfile,
+ sex_info_file_key,
+ new_cdata,
+ *make_process_data_covar(cdata)):
+ yield {
+ key: thread_op(value, partial(replace_sex_info, cdata=cdata))
+ for key, value in row.items() if key not in ci_fields}