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authorFrederick Muriuki Muriithi2024-02-13 04:03:02 +0300
committerFrederick Muriuki Muriithi2024-02-13 04:03:02 +0300
commit8b637a760362d08fb92152288d0b04f90299da5f (patch)
tree55b9900a72f51902cd5c6150cdab3f0cd097c372 /r_qtl
parent092ae35512b3ef236622c4ab9dfe2bafb221ded7 (diff)
downloadgn-uploader-8b637a760362d08fb92152288d0b04f90299da5f.tar.gz
Make "FILE_TYPES" part of public interface for module/package.
Diffstat (limited to 'r_qtl')
-rw-r--r--r_qtl/r_qtl2.py4
-rw-r--r--r_qtl/r_qtl2_qc.py6
2 files changed, 5 insertions, 5 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index e74312f..0241458 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -12,7 +12,7 @@ from functional_tools import take, chain
from r_qtl.errors import InvalidFormat, MissingFileError
-__FILE_TYPES__ = (
+FILE_TYPES = (
"geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap",
"phenose")
@@ -33,7 +33,7 @@ def control_data(zfile: ZipFile) -> dict:
"comment.char": "#",
"sep": ",",
**{
- f"{key}_transposed": False for key in __FILE_TYPES__
+ f"{key}_transposed": False for key in FILE_TYPES
},
**(json.loads(zfile.read(files[0]))
if files[0].endswith(".json")
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index aa5c81e..43f7d94 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -5,7 +5,7 @@ from typing import Union, Iterator, Optional, Callable
from r_qtl import errors as rqe
from r_qtl import r_qtl2 as rqtl2
-from r_qtl.r_qtl2 import __FILE_TYPES__
+from r_qtl.r_qtl2 import FILE_TYPES
from r_qtl.fileerrors import MissingFile
from quality_control.errors import InvalidValue
@@ -21,7 +21,7 @@ def bundle_files_list(cdata: dict) -> tuple[tuple[str, str], ...]:
fileslist: tuple[tuple[str, str], ...] = reduce(
__merge__,
- (key for key in cdata.keys() if key in __FILE_TYPES__),
+ (key for key in cdata.keys() if key in FILE_TYPES),
tuple())
if "file" in cdata.get("sex", {}):
@@ -98,7 +98,7 @@ def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]
def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[
Union[InvalidValue, MissingFile]]:
"""Check for and retrieve errors from files of type `filetype`."""
- assert filetype in __FILE_TYPES__, f"Invalid file type {filetype}."
+ assert filetype in FILE_TYPES, f"Invalid file type {filetype}."
cdata = rqtl2.control_data(zfile)
try:
for lineno, row in enumerate(