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"""The R/qtl2 parsing and processing code."""
import io
import csv
import json
import yaml
from pathlib import Path
from functools import reduce
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)
def control_data(zfile: ZipFile) -> dict:
"""Retrieve the control file from the zip file info."""
files = tuple(filename
for filename in zfile.namelist()
if (filename.endswith(".yaml") or filename.endswith(".json")))
num_files = len(files)
if num_files == 0:
raise InvalidFormat("Expected a json or yaml control file.")
if num_files > 1:
raise InvalidFormat("Found more than one possible control file.")
return (json.loads(zfile.read(files[0]))
if files[0].endswith(".json")
else yaml.safe_load(zfile.read(files[0])))
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):
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:
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,
replace_na_strings)
for key,value
in row.items()
}
def __merge__(key, samples, line):
marker = line[0]
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", ","))
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:]
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) -> 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[{
"genetic-map": "gmap",
"physical-map": "pmap"
}[map_type]]
transposed_dict = {
"genetic-map": "gmap_transposed",
"physical-map": "pmap_transposed"
}
if not cdata.get(transposed_dict[map_type], False):
with zfile.open(map_file) as gmapfile:
reader = csv.DictReader(
filter(lambda line: not line.startswith("#"),
io.TextIOWrapper(gmapfile)),
delimiter=cdata.get("sep", ","))
return tuple(row for row in reader)
with zfile.open(map_file) as gmapfile:
lines = [[field.strip() for field in
line.strip().split(cdata.get("sep", ","))]
for line in
filter(lambda line: not line.startswith("#"),
io.TextIOWrapper(gmapfile))]
headers = tuple(line[0] for line in lines)
return reduce(
lambda gmap, row: gmap + (dict(zip(headers, row)),),
zip(*(line[1:] for line in lines)),
tuple())
def read_r_qtl2_files(filepath: Path):
"""Read R/qtl2 format zip files."""
with ZipFile(filepath, "r") as zfile:
cf = control_data(zfile)
raise NotImplementedError("Implementation is incomplete.")
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