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
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
|
#!/usr/bin/env python3
"""A script that generates the genotype files for groups of individuals, using an existing strain genotype file as a basis
Example commands:
python3 gen_ind_genofiles.py
/home/zas1024/gn2-zach/genotype_files/genotype/
/home/zas1024/gn2-zach/new_geno/
BXD-Micturition.geno
BXD.json
python3 gen_ind_genofiles.py
/home/zas1024/gn2-zach/genotype_files/genotype
/home/zas1024/gn2-zach/new_geno/
BXD-Micturition.geno
BXD.2.geno BXD.4.geno BXD.5.geno
"""
import json
import os
import sys
from typing import List
import MySQLdb
def conn():
return MySQLdb.Connect(db=os.environ.get("DB_NAME"),
user=os.environ.get("DB_USER"),
passwd=os.environ.get("DB_PASS"),
host=os.environ.get("DB_HOST"))
def main(args):
# Directory in which .geno files are located
geno_dir = args[1]
# Directory in which to output new files
out_dir = args[2]
# The individuals group that we want to generate a .geno file for
target_file = geno_dir + args[3]
# The source group(s) we're generating the .geno files from
# This can be passed as either a specific .geno file (or set of files as multiple arguments),
# or as a JSON file containing a set of .geno files (and their corresponding file names and sample lists)
geno_json = {}
source_files = []
if ".json" in args[4]:
geno_json = json.load(open(geno_dir + args[4], "r"))
par_f1s = {
"mat": geno_json['mat'],
"pat": geno_json['pat'],
"f1s": geno_json['f1s']
}
# List of file titles and locations from JSON
source_files = [{'title': genofile['title'], 'location': geno_dir + genofile['location']} for genofile in geno_json['genofile']]
else:
par_f1s = {}
# List of files directly taken from command line arguments, with titles just set to the filename
for group in args[4:]:
file_name = geno_dir + group + ".geno" if ".geno" not in group else group
source_files.append({'title': file_name[:-5], 'location': file_name})
if len(source_files) > 1:
# Generate a JSON file pointing to the new target genotype files, in situations where there are multiple source .geno files
target_json_loc = out_dir + ".".join(args[3].split(".")[:-1]) + ".json"
target_json = {'genofile': []}
# Generate the output .geno files
for source_file in source_files:
filename, samples = generate_new_genofile(source_file['location'], target_file, par_f1s, out_dir)
target_json['genofile'].append({
'location': filename.split("/")[-1],
'title': source_file['title'],
'sample_list': samples
})
json.dump(target_json, open(target_json_loc, "w"))
def get_strain_for_sample(sample):
query = (
"SELECT CaseAttributeXRefNew.Value "
"FROM CaseAttributeXRefNew, Strain "
"WHERE CaseAttributeXRefNew.CaseAttributeId=11 "
"AND CaseAttributeXRefNew.StrainId = Strain.Id "
"AND Strain.Name = %(name)s" )
with conn().cursor() as cursor:
cursor.execute(query, {"name": sample.strip()})
return cursor.fetchone()[0]
def generate_new_genofile(source_genofile, target_genofile, par_f1s, out_dir):
source_samples = group_samples(source_genofile)
source_genotypes = strain_genotypes(source_genofile)
target_samples = group_samples(target_genofile)
strain_pos_map = map_strain_pos_to_target_group(source_samples, target_samples, par_f1s)
if len(source_genofile.split("/")[-1].split(".")) > 2:
# The number in the source genofile; for example 4 in BXD.4.geno
source_num = source_genofile.split("/")[-1].split(".")[-2]
target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + "." + source_num + ".geno"
else:
target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + ".geno"
file_location = out_dir + target_filename
with open(file_location, "w") as fh:
for metadata in ["name", "type", "mat", "pat", "het", "unk"]:
fh.write("@" + metadata + ":" + source_genotypes[metadata] + "\n")
header_line = ["Chr", "Locus", "cM", "Mb"] + target_samples
fh.write("\t".join(header_line))
for marker in source_genotypes['markers']:
line_items = [
marker['Chr'],
marker['Locus'],
marker['cM'],
marker['Mb']
]
for pos in strain_pos_map:
if isinstance(pos, int):
line_items.append(marker['genotypes'][pos])
else:
if pos in ["mat", "pat"]:
line_items.append(source_genotypes[pos])
elif pos == "f1s":
line_items.append("H")
else:
line_items.append("U")
fh.write("\t".join(line_items) + "\n")
return file_location, target_samples
def map_strain_pos_to_target_group(source_samples, target_samples, par_f1s):
"""
Retrieve corresponding strain position for each sample in the target group
This is so the genotypes from the base genofile can be mapped to the samples in the target group
For example:
Base strains: BXD1, BXD2, BXD3
Target samples: BXD1_1, BXD1_2, BXD2_1, BXD3_1, BXD3_2, BXD3_3
Returns: [0, 0, 1, 2, 2, 2]
"""
pos_map = []
for sample in target_samples:
sample_strain = get_strain_for_sample(sample)
if sample_strain in source_samples:
pos_map.append(source_samples.index(sample_strain))
else:
val = "U"
for key in par_f1s.keys():
if sample_strain in par_f1s[key]:
val = key
pos_map.append(val)
return pos_map
def group_samples(target_file: str) -> List:
"""
Get the group samples from its "dummy" .geno file (which still contains the sample list)
"""
sample_list = []
with open(target_file, "r") as target_geno:
for i, line in enumerate(target_geno):
# Skip header lines
if line[0] in ["#", "@"] or not len(line):
continue
line_items = line.split("\t")
sample_list = [item for item in line_items if item not in ["Chr", "Locus", "Mb", "cM"]]
break
return sample_list
def strain_genotypes(strain_genofile: str) -> List:
"""
Read genotypes from source strain .geno file
:param strain_genofile: string of genofile filename
:return: a list of dictionaries representing each marker's genotypes
Example output: [
{
'Chr': '1',
'Locus': 'marker1',
'Mb': '10.0',
'cM': '8.0',
'genotypes': [('BXD1', 'B'), ('BXD2', 'D'), ('BXD3', 'H'), ...]
},
...
]
"""
geno_dict = {}
geno_start_col = None
header_columns = []
sample_list = []
markers = []
with open(strain_genofile, "r") as source_geno:
for i, line in enumerate(source_geno):
if line[0] == "@":
metadata_type = line[1:].split(":")[0]
if metadata_type in ['name', 'type', 'mat', 'pat', 'het', 'unk']:
geno_dict[metadata_type] = line.split(":")[1].strip()
continue
# Skip other header lines
if line[0] == "#" or not len(line):
continue
line_items = line.split("\t")
if "Chr" in line_items: # Header row
# Get the first column index containing genotypes
header_columns = line_items
for j, item in enumerate(line_items):
if item not in ["Chr", "Locus", "Mb", "cM"]:
geno_start_col = j
break
sample_list = line_items[geno_start_col:]
if not geno_start_col:
print("Check .geno file - expected columns not found")
sys.exit()
else: # Marker rows
this_marker = {
'Chr': line_items[header_columns.index("Chr")],
'Locus': line_items[header_columns.index("Locus")],
'Mb': line_items[header_columns.index("Mb")],
'cM': line_items[header_columns.index("cM")],
'genotypes': [item.strip() for item in line_items][geno_start_col:]
}
markers.append(this_marker)
geno_dict['markers'] = markers
return geno_dict
if __name__ == "__main__":
print("command line arguments:\n\t%s" % sys.argv)
main(sys.argv)
|
