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"""The R/qtl2 parsing and processing code."""
import io
import csv
import json
from zipfile import ZipFile
from functools import reduce
from typing import Iterator, Iterable, Callable
import yaml
from quality_control.parsing import take
from r_qtl.errors import InvalidFormat
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 with_non_transposed(zfile: ZipFile,
member_key: str,
cdata: dict,
process_value: Callable[
[dict], dict] = lambda val: val) -> Iterator[dict]:
"""Process non-transposed file values
Arguments:
zfile: A zipfile object from opening a R/qtl2 bundle.
member_key: A key to retrieve the member file to process from the file.
cdata: The control data from the R/qtl2 bundle read from the JSON/YAML file.
process_value: A function to process the values from the file.
"""
def not_comment_line(line):
return not line.startswith(cdata.get("comment.char", "#"))
with zfile.open(cdata[member_key]) as innerfile:
reader = csv.DictReader(
filter(not_comment_line, io.TextIOWrapper(innerfile)),
delimiter=cdata.get("sep", ","))
for row in reader:
yield process_value(row)
def __make_organise_by_id__(id_key):
"""Return a function to use with `reduce` to organise values by some
identifier."""
def __organiser__(acc, item):
row = acc.get(item[id_key], {})
return {**acc, item[id_key]: {**row, **item}}
return __organiser__
def __batch_of_n__(iterable: Iterable, num):
"""Return a batch of `num` items or less from the `iterable`."""
while True:
items = take(iterable, num)
if len(items) <= 0:
break
yield items
def with_transposed(zfile: ZipFile,
member_key: str,
cdata: dict,
process_value: Callable[
[str, tuple[str, ...], tuple[str, ...]],
tuple[dict, ...]]) -> Iterator[dict]:
"""Process transposed file values
Arguments:
zfile: A zipfile object from opening a R/qtl2 bundle.
member_key: A key to retrieve the member file to process from the file.
cdata: The control data from the R/qtl2 bundle read from the JSON/YAML file.
process_value: A function to process the values from the file.
"""
with zfile.open(cdata[member_key]) as innerfile:
lines = (tuple(field.strip() for field in
line.strip().split(cdata.get("sep", ",")))
for line in
filter(lambda line: not line.startswith("#"),
io.TextIOWrapper(innerfile)))
try:
id_line = next(lines)
id_key, headers = id_line[0], id_line[1:]
for _key, row in reduce(# type: ignore[var-annotated]
__make_organise_by_id__(id_key),
(row
for batch in __batch_of_n__(lines, 300)
for line in batch
for row in process_value(id_key, headers, line)),
{}).items():
yield row
except StopIteration:
pass
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):
for line in with_non_transposed(
zfile,
"geno",
cdata,
lambda row: {
key: thread_op(value, replace_genotype_codes, replace_na_strings)
for key,value in row.items()
}):
yield line
return None
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:]))
for row in with_transposed(zfile, "geno", cdata, __merge__):
yield row
def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> Iterator[dict]:
"""Read gmap files to get the genome mapping data"""
assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
map_file_key = {
"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):
for row in with_non_transposed(zfile, map_file_key, cdata):
yield row
return None
def __merge__(key, samples, line):
marker = line[0]
return tuple(dict(zip([key, marker], items))
for items in zip(samples, line[1:]))
for row in with_transposed(zfile, map_file_key, cdata, __merge__):
yield row
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