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
179
180
181
182
183
184
|
"""Genotype utilities"""
import os
import gzip
from typing import Union
from pathlib import Path
def build_genotype_file(geno_name: str,
base_dir: Union[str, Path],
extension: str = "geno"):
"""Build the absolute path for the genotype file."""
return f"{os.path.abspath(base_dir)}/{geno_name}.{extension}"
def load_genotype_samples(genotype_filename: str, file_type: str = "geno"):
"""
Load sample of samples from genotype files.
DESCRIPTION:
Traits can contain a varied number of samples, some of which do not exist in
certain genotypes. In order to compute QTLs, GEMMAs, etc, we need to ensure
to pick only those samples that exist in the genotype under consideration
for the traits used in the computation.
This function loads a list of samples from the genotype files for use in
filtering out unusable samples.
PARAMETERS:
genotype_filename: The absolute path to the genotype file to load the
samples from.
file_type: The type of file. Currently supported values are 'geno' and
'plink'.
"""
file_type_fns = {
"geno": __load_genotype_samples_from_geno,
"plink": __load_genotype_samples_from_plink
}
return file_type_fns[file_type](genotype_filename)
def __load_genotype_samples_from_geno(genotype_filename: str):
"""
Helper function for `load_genotype_samples` function.
Loads samples from '.geno' files.
"""
def __remove_comments_and_empty_lines__(rows):
return(
line for line in rows
if line and not line.startswith(("#", "@")))
gzipped_filename = f"{genotype_filename}.gz"
if os.path.isfile(gzipped_filename):
with gzip.open(gzipped_filename) as gz_genofile:
rows = __remove_comments_and_empty_lines__(gz_genofile.readlines())
else:
with open(genotype_filename, encoding="utf8") as genofile:
rows = __remove_comments_and_empty_lines__(genofile.readlines())
headers = next(rows).split() # type: ignore[arg-type]
if headers[3] == "Mb":
return tuple(headers[4:])
return tuple(headers[3:])
def __load_genotype_samples_from_plink(genotype_filename: str):
"""
Helper function for `load_genotype_samples` function.
Loads samples from '.plink' files.
"""
with open(genotype_filename, encoding="utf8") as genofile:
return tuple(line.split()[1] for line in genofile)
def parse_genotype_labels(lines: list):
"""
Parse label lines into usable genotype values
DESCRIPTION:
Reworks
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L75-L93
"""
acceptable_labels = ["name", "filler", "type", "mat", "pat", "het", "unk"]
def __parse_label(line):
label, value = [l.strip() for l in line[1:].split(":")]
if label not in acceptable_labels:
return None
if label == "name":
return ("group", value)
return (label, value)
return tuple(
item for item in (__parse_label(line) for line in lines)
if item is not None)
def parse_genotype_header(line: str, parlist: tuple = tuple()):
"""
Parse the genotype file header line
DESCRIPTION:
Reworks
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L94-L114
"""
items = [item.strip() for item in line.split("\t")]
mbmap = "Mb" in items
prgy = ((parlist + tuple(items[4:])) if mbmap
else (parlist + tuple(items[3:])))
return (
("Mbmap", mbmap),
("cm_column", items.index("cM")),
("mb_column", None if not mbmap else items.index("Mb")),
("prgy", prgy),
("nprgy", len(prgy)))
def parse_genotype_marker(line: str, geno_obj: dict, parlist: tuple):
"""
Parse a data line in a genotype file
DESCRIPTION:
Reworks
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L143-L190
"""
# pylint: disable=W0702
marker_row = [item.strip() for item in line.split("\t")]
geno_table = {
geno_obj["mat"]: -1, geno_obj["pat"]: 1, geno_obj["het"]: 0,
geno_obj["unk"]: "U"
}
start_pos = 4 if geno_obj["Mbmap"] else 3
if len(parlist) > 0:
start_pos = start_pos + 2
alleles = marker_row[start_pos:]
genotype = tuple(
(geno_table[allele] if allele in geno_table else "U")
for allele in alleles)
if len(parlist) > 0:
genotype = (-1, 1) + genotype
try:
cm_val = float(geno_obj["cm_column"])
except:
if geno_obj["Mbmap"]:
cm_val = float(geno_obj["mb_column"])
else:
cm_val = 0
return (
("chr", marker_row[0]),
("name", marker_row[1]),
("cM", cm_val),
("Mb", float(geno_obj["mb_column"]) if geno_obj["Mbmap"] else None),
("genotype", genotype))
def build_genotype_chromosomes(geno_obj, markers):
"""
Build up the chromosomes from the given markers and partially built geno
object
"""
mrks = [dict(marker) for marker in markers]
chr_names = {marker["chr"] for marker in mrks}
return tuple((
("name", chr_name), ("mb_exists", geno_obj["Mbmap"]), ("cm_column", 2),
("mb_column", geno_obj["mb_column"]),
("loci", tuple(marker for marker in mrks if marker["chr"] == chr_name)))
for chr_name in sorted(chr_names))
def parse_genotype_file(filename: str, parlist: tuple = tuple()):
"""
Parse the provided genotype file into a usable pytho3 data structure.
"""
with open(filename, "r", encoding="utf8") as infile:
contents = infile.readlines()
lines = tuple(line for line in contents if
((not line.strip().startswith("#")) and
(not line.strip() == "")))
labels = parse_genotype_labels(
[line for line in lines if line.startswith("@")])
data_lines = tuple(line for line in lines if not line.startswith("@"))
header = parse_genotype_header(data_lines[0], parlist)
geno_obj = dict(labels + header)
markers = (
parse_genotype_marker(line, geno_obj, parlist)
for line in data_lines[1:])
chromosomes = tuple(
dict(chromosome) for chromosome in
build_genotype_chromosomes(geno_obj, tuple(markers)))
return {**geno_obj, "chromosomes": chromosomes}
|
