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-rw-r--r--mypy.ini3
-rw-r--r--r_qtl/r_qtl2.py46
-rw-r--r--tests/r_qtl/test_r_qtl2_geno.py125
3 files changed, 101 insertions, 73 deletions
diff --git a/mypy.ini b/mypy.ini
index b0c3b7b..08e896e 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -25,4 +25,7 @@ ignore_missing_imports = True
ignore_missing_imports = True
[mypy-MySQLdb.*]
+ignore_missing_imports = True
+
+[mypy-yaml.*]
ignore_missing_imports = True \ No newline at end of file
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 47f101e..ec7a954 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -5,11 +5,13 @@ import json
import yaml
from pathlib import Path
from functools import reduce
-from typing import Any, List, Union, Iterator
from zipfile import ZipFile, ZipInfo, is_zipfile
+from typing import Any, List, Union, Iterator, Iterable
from r_qtl.errors import InvalidFormat
+from quality_control.parsing import take
+
def thread_op(value, *functions):
"""Thread the `value` through the sequence of `functions`."""
return reduce(lambda result, func: func(result), functions, value)
@@ -30,25 +32,16 @@ def control_data(zfile: ZipFile) -> dict:
if files[0].endswith(".json")
else yaml.safe_load(zfile.read(files[0])))
-def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict:
- """Read Individual ID key and the marker names."""
- line_num = 0
- with zfile.open(cdata["geno"]) as genofile:
- for line in filter(lambda line: not line.startswith("#"),
- io.TextIOWrapper(genofile)):
- line_parts = line.strip().split(cdata.get("sep", ","))
- return {
- "individual_id_key": line_parts[0].strip(),
- "markers": tuple(marker.strip() for marker in line_parts[1:])
- }
-
def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
"""Load the genotype file, making use of the control data."""
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)
+ nastrings = cdata.get("na.strings")
+ if bool(nastrings):
+ return (None if val in nastrings else val)
+ return val
if not cdata.get("geno_transposed", False):
with zfile.open(cdata["geno"]) as genofile:
@@ -68,13 +61,20 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
def __merge__(key, samples, line):
marker = line[0]
- return (
+ return tuple(
dict(zip(
[key, marker],
(thread_op(item, replace_genotype_codes, replace_na_strings)
for item in items)))
for items in zip(samples, line[1:]))
+ def __n_batch__(iterable: Iterable, num):
+ while True:
+ items = take(iterable, num)
+ if len(items) <= 0:
+ break
+ yield items
+
if cdata.get("geno_transposed", False):
with zfile.open(cdata["geno"]) as genofile:
lines = (line.strip().split(cdata.get("sep", ","))
@@ -82,11 +82,19 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
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 __organise_by_id__(acc, item):
+ row = acc.get(item[id_key], {})
+ return {**acc, item[id_key]: {**row, **item}}
+ for _key, row in reduce(# type: ignore[var-annotated]
+ __organise_by_id__,
+ (row
+ for batch in __n_batch__(lines, 300)
+ for line in batch
+ for row in __merge__(id_key, samples, line)),
+ {}).items():
+ yield row
-def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
+def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> tuple[dict, ...]:
"""Read gmap files to get the genome mapping data"""
assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
map_file = cdata[{
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 908ef55..7b660a6 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -92,60 +92,77 @@ from r_qtl import r_qtl2 as rqtl2
"EC.66C": 2
})),
("tests/r_qtl/test_files/test_geno_transposed.zip",
- ({"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}))))
+ ({
+ "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
+ }))))
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 21:11:16 +0000