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
|
"""This class contains functions relating to trait data manipulation"""
from typing import Any, Dict, Union
def get_trait_csv_sample_data(conn: Any,
trait_name: int, phenotype_id: int):
"""Fetch a trait and return it as a csv string"""
sql = ("SELECT Strain.Id, PublishData.Id, Strain.Name, "
"PublishData.value, "
"PublishSE.error, NStrain.count FROM "
"(PublishData, Strain, PublishXRef, PublishFreeze) "
"LEFT JOIN PublishSE ON "
"(PublishSE.DataId = PublishData.Id AND "
"PublishSE.StrainId = PublishData.StrainId) "
"LEFT JOIN NStrain ON (NStrain.DataId = PublishData.Id AND "
"NStrain.StrainId = PublishData.StrainId) WHERE "
"PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
"PublishData.Id = PublishXRef.DataId AND "
"PublishXRef.Id = %s AND PublishXRef.PhenotypeId = %s "
"AND PublishData.StrainId = Strain.Id Order BY Strain.Name")
csv_data = ["Strain Id,Strain Name,Value,SE,Count"]
publishdata_id = ""
with conn.cursor() as cursor:
cursor.execute(sql, (trait_name, phenotype_id,))
for record in cursor.fetchall():
(strain_id, publishdata_id,
strain_name, value, error, count) = record
csv_data.append(
",".join([str(val) if val else "x"
for val in (strain_id, strain_name,
value, error, count)]))
return f"# Publish Data Id: {publishdata_id}\n\n" + "\n".join(csv_data)
def update_sample_data(conn: Any,
strain_name: str,
strain_id: int,
publish_data_id: int,
value: Union[int, float, str],
error: Union[int, float, str],
count: Union[int, str]):
"""Given the right parameters, update sample-data from the relevant
table."""
STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
"WHERE StrainId = %s AND Id = %s")
PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
"WHERE StrainId = %s AND DataId = %s")
N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s")
updated_strains: int = 0
updated_published_data: int = 0
updated_se_data: int = 0
updated_n_strains: int = 0
with conn.cursor() as cursor:
# Update the Strains table
cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id))
updated_strains: int = cursor.rowcount
# Update the PublishData table
cursor.execute(PUBLISH_DATA_SQL,
(None if value == "x" else value,
strain_id, publish_data_id))
updated_published_data: int = cursor.rowcount
# Update the PublishSE table
cursor.execute(PUBLISH_SE_SQL,
(None if error == "x" else error,
strain_id, publish_data_id))
updated_se_data: int = cursor.rowcount
# Update the NStrain table
cursor.execute(N_STRAIN_SQL,
(None if count == "x" else count,
strain_id, publish_data_id))
updated_n_strains: int = cursor.rowcount
return (updated_strains, updated_published_data,
updated_se_data, updated_n_strains)
def retrieve_trait_dataset_name(
trait_type: str, threshold: int, name: str, connection: Any):
"""
Retrieve the name of a trait given the trait's name
This is extracted from the `webqtlDataset.retrieveName` function as is
implemented at
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
"""
columns = "Id, Name, FullName, ShortName{}".format(
", DataScale" if trait_type == "ProbeSet" else "")
query = (
"SELECT {columns} "
"FROM {trait_type}Freeze "
"WHERE "
"public > %(threshold)s "
"AND "
"(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
columns=columns, trait_type=trait_type)
with connection.cursor() as cursor:
cursor.execute(query, {"threshold": threshold, "name": name})
return cursor.fetchone()
PUBLISH_TRAIT_INFO_QUERY = (
"SELECT "
"PublishXRef.Id, Publication.PubMed_ID, "
"Phenotype.Pre_publication_description, "
"Phenotype.Post_publication_description, "
"Phenotype.Original_description, "
"Phenotype.Pre_publication_abbreviation, "
"Phenotype.Post_publication_abbreviation, "
"Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
"Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
"Publication.Title, Publication.Abstract, Publication.Journal, "
"Publication.Volume, Publication.Pages, Publication.Month, "
"Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
"PublishXRef.comments "
"FROM "
"PublishXRef, Publication, Phenotype, PublishFreeze "
"WHERE "
"PublishXRef.Id = %(trait_name)s AND "
"Phenotype.Id = PublishXRef.PhenotypeId AND "
"Publication.Id = PublishXRef.PublicationId AND "
"PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
"PublishFreeze.Id =%(trait_dataset_id)s")
def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `Publish` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
with conn.cursor() as cursor:
cursor.execute(
PUBLISH_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_id"]
})
return cursor.fetchone()
PROBESET_TRAIT_INFO_QUERY = (
"SELECT "
"ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
"ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, "
"ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, "
"ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
"ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
"ProbeSet.strand_probe, ProbeSet.strand_gene, "
"ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
"ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, "
"ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, "
"ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
"ProbeSet.flag "
"FROM "
"ProbeSet, ProbeSetFreeze, ProbeSetXRef "
"WHERE "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
"ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
"ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
"ProbeSet.Name = %(trait_name)s")
def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `ProbeSet` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
with conn.cursor() as cursor:
cursor.execute(
PROBESET_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_name"]
})
return cursor.fetchone()
GENO_TRAIT_INFO_QUERY = (
"SELECT "
"Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
"FROM "
"Geno, GenoFreeze, GenoXRef "
"WHERE "
"GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
"GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s")
def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `Geno` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
with conn.cursor() as cursor:
cursor.execute(
GENO_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_name"]
})
return cursor.fetchone()
TEMP_TRAIT_INFO_QUERY = (
"SELECT name, description FROM Temp "
"WHERE Name = %(trait_name)s")
def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `Temp` traits.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
with conn.cursor() as cursor:
cursor.execute(
TEMP_TRAIT_INFO_QUERY,
{
k:v for k, v in trait_data_source.items()
if k in ["trait_name"]
})
return cursor.fetchone()
def retrieve_trait_info(
trait_type: str, trait_name: str, trait_dataset_id: int,
trait_dataset_name: str, conn: Any):
"""Retrieves the trait information.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
This function, or the dependent functions, might be incomplete as they are
currently."""
trait_info_function_table = {
"Publish": retrieve_publish_trait_info,
"ProbeSet": retrieve_probeset_trait_info,
"Geno": retrieve_geno_trait_info,
"Temp": retrieve_temp_trait_info
}
return trait_info_function_table[trait_type](
{
"trait_name": trait_name,
"trait_dataset_id": trait_dataset_id,
"trait_dataset_name":trait_dataset_name
},
conn)
|
