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-rw-r--r--r_qtl/r_qtl2.py50
-rw-r--r--tests/r_qtl/test_r_qtl2_geno.py134
2 files changed, 88 insertions, 96 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index e019d99..47f101e 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -32,7 +32,6 @@ def control_data(zfile: ZipFile) -> dict:
def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict:
"""Read Individual ID key and the marker names."""
- # TODO: Handle transposed files
line_num = 0
with zfile.open(cdata["geno"]) as genofile:
for line in filter(lambda line: not line.startswith("#"),
@@ -45,25 +44,48 @@ def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict:
def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
"""Load the genotype file, making use of the control data."""
- # TODO: Handle transposed files
- with zfile.open(cdata["geno"]) as genofile:
- reader = csv.DictReader(filter(lambda line: not line.startswith("#"),
- io.TextIOWrapper(genofile)),
- delimiter=cdata.get("sep", ","))
- if not cdata.get("geno_transposed", False):
+ def replace_genotype_codes(val):
+ return cdata["genotypes"].get(val, val)
+
+ def replace_na_strings(val):
+ return (None if val in cdata["na.strings"] else val)
+
+ if not cdata.get("geno_transposed", False):
+ with zfile.open(cdata["geno"]) as genofile:
+ reader = csv.DictReader(
+ filter(lambda line: not line.startswith("#"),
+ io.TextIOWrapper(genofile)),
+ delimiter=cdata.get("sep", ","))
for row in reader:
yield {
key: thread_op(
value,
- # replace genotype codes
- lambda val: cdata["genotypes"].get(val, val),
- # replace N/A strings
- lambda val: (
- None if val in cdata["na.strings"] else val))
+ replace_genotype_codes,
+ replace_na_strings)
for key,value
in row.items()
}
+ def __merge__(key, samples, line):
+ marker = line[0]
+ return (
+ dict(zip(
+ [key, marker],
+ (thread_op(item, replace_genotype_codes, replace_na_strings)
+ for item in items)))
+ for items in zip(samples, line[1:]))
+
+ if cdata.get("geno_transposed", False):
+ with zfile.open(cdata["geno"]) as genofile:
+ lines = (line.strip().split(cdata.get("sep", ","))
+ for line in filter(lambda line: not line.startswith("#"),
+ io.TextIOWrapper(genofile)))
+ id_line = next(lines)
+ id_key, samples = id_line[0], id_line[1:]
+ for line in lines:
+ for row in __merge__(id_key, samples, line):
+ yield row
+
def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
"""Read gmap files to get the genome mapping data"""
assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
@@ -71,10 +93,6 @@ def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
"genetic-map": "gmap",
"physical-map": "pmap"
}[map_type]]
- # TODO: Might need to check `gmap_transposed` and `pmap_transposed` instead
- # of `geno_transposed` -- see
- # https://github.com/rqtl/qtl2data/blob/main/ArabMAGIC/arabmagic_tair8.json
- # for the *_transposed values
transposed_dict = {
"genetic-map": "gmap_transposed",
"physical-map": "pmap_transposed"
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 5ebb5a9..908ef55 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -92,86 +92,60 @@ from r_qtl import r_qtl2 as rqtl2
"EC.66C": 2
})),
("tests/r_qtl/test_files/test_geno_transposed.zip",
- ({
- "id": "1",
- "PVV4": 1,
- "AXR-1": 1,
- "HH.335C-Col/PhyA": 1,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "2",
- "PVV4": 1,
- "AXR-1": 1,
- "HH.335C-Col/PhyA": 1,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "3",
- "PVV4": 2,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": None,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "4",
- "PVV4": 1,
- "AXR-1": 1,
- "HH.335C-Col/PhyA": 1,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "5",
- "PVV4": 2,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": 2,
- "EC.480C": 2,
- "EC.66C": 2
- },
- {
- "id": "6",
- "PVV4": 2,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": 2,
- "EC.480C": 2,
- "EC.66C": 2
- },
- {
- "id": "7",
- "PVV4": 1,
- "AXR-1": 1,
- "HH.335C-Col/PhyA": 1,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "8",
- "PVV4": 2,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": 2,
- "EC.480C": 1,
- "EC.66C": 1
- },
- {
- "id": "9",
- "PVV4": None,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": 2,
- "EC.480C": 2,
- "EC.66C": 2
- },
- {
- "id": "10",
- "PVV4": 2,
- "AXR-1": 2,
- "HH.335C-Col/PhyA": 2,
- "EC.480C": 2,
- "EC.66C": 2
- }))))
+ ({"id": "1", "PVV4": 1},
+ {"id": "2", "PVV4": 1},
+ {"id": "3", "PVV4": 2},
+ {"id": "4", "PVV4": 1},
+ {"id": "5", "PVV4": 2},
+ {"id": "6", "PVV4": 2},
+ {"id": "7", "PVV4": 1},
+ {"id": "8", "PVV4": 2},
+ {"id": "9", "PVV4": None},
+ {"id": "10", "PVV4": 2},
+
+ {"id": "1", "AXR-1": 1},
+ {"id": "2", "AXR-1": 1},
+ {"id": "3", "AXR-1": 2},
+ {"id": "4", "AXR-1": 1},
+ {"id": "5", "AXR-1": 2},
+ {"id": "6", "AXR-1": 2},
+ {"id": "7", "AXR-1": 1},
+ {"id": "8", "AXR-1": 2},
+ {"id": "9", "AXR-1": 2},
+ {"id": "10", "AXR-1": 2},
+
+ {"id": "1", "HH.335C-Col/PhyA": 1},
+ {"id": "2", "HH.335C-Col/PhyA": 1},
+ {"id": "3", "HH.335C-Col/PhyA": None},
+ {"id": "4", "HH.335C-Col/PhyA": 1},
+ {"id": "5", "HH.335C-Col/PhyA": 2},
+ {"id": "6", "HH.335C-Col/PhyA": 2},
+ {"id": "7", "HH.335C-Col/PhyA": 1},
+ {"id": "8", "HH.335C-Col/PhyA": 2},
+ {"id": "9", "HH.335C-Col/PhyA": 2},
+ {"id": "10", "HH.335C-Col/PhyA": 2},
+
+ {"id": "1", "EC.480C": 1},
+ {"id": "2", "EC.480C": 1},
+ {"id": "3", "EC.480C": 1},
+ {"id": "4", "EC.480C": 1},
+ {"id": "5", "EC.480C": 2},
+ {"id": "6", "EC.480C": 2},
+ {"id": "7", "EC.480C": 1},
+ {"id": "8", "EC.480C": 1},
+ {"id": "9", "EC.480C": 2},
+ {"id": "10", "EC.480C": 2},
+
+ {"id": "1","EC.66C": 1},
+ {"id": "2", "EC.66C": 1},
+ {"id": "3", "EC.66C": 1},
+ {"id": "4", "EC.66C": 1},
+ {"id": "5", "EC.66C": 2},
+ {"id": "6", "EC.66C": 2},
+ {"id": "7", "EC.66C": 1},
+ {"id": "8", "EC.66C": 1},
+ {"id": "9", "EC.66C": 2},
+ {"id": "10", "EC.66C": 2}))))
def test_parse_geno_files(relpath,expected):
"""
GIVEN: Path to a zip file with R/qtl2 data
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-04 21:30:34 +0000