1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
|
"""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
def phenotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
"""Load phenotype file data."""
if not cdata.get("pheno_transposed", False):
for row in with_non_transposed(zfile, "pheno", cdata, lambda val: val):
yield row
return
def __merge__(id_key, ids, vals):
return tuple(dict(zip([id_key, vals[0]], items))
for items in zip(ids, vals[1:]))
for row in with_transposed(zfile, "pheno", cdata, __merge__):
yield row
|
