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
|
import re
import itertools
from flask import g
from base import webqtlCaseData
from pprint import pformat as pf
from utility import Plot
from utility import Bunch
class SampleList(object):
def __init__(self,
dataset,
sample_names,
this_trait,
sample_group_type="primary",
header="Samples"):
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
self.sample_attribute_values = {}
self.get_attributes()
if self.this_trait and self.dataset:
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
# ZS: self.this_trait will be a list if it is a Temp trait
if isinstance(self.this_trait, list):
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
if counter <= len(self.this_trait):
if isinstance(self.this_trait[counter-1], (bytes, bytearray)):
if (self.this_trait[counter-1].decode("utf-8").lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
value=float(self.this_trait[counter-1]))
else:
if (self.this_trait[counter-1].lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
value=float(self.this_trait[counter-1]))
else:
# ZS - If there's no value for the sample/strain,
# create the sample object (so samples with no value
# are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
if (self.dataset.group.name == 'AXBXA' and
sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
sample.this_id = str(counter)
# ZS: For extra attribute columns; currently only used by
# several datasets
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
self.sample_list.append(sample)
self.se_exists = any(sample.variance for sample in self.sample_list)
self.num_cases_exists = any(
sample.num_cases for sample in self.sample_list)
first_attr_col = self.get_first_attr_col()
for sample in self.sample_list:
sample.first_attr_col = first_attr_col
self.do_outliers()
def __repr__(self):
return "<SampleList> --> %s" % (pf(self.__dict__))
def do_outliers(self):
values = [sample.value for sample in self.sample_list
if sample.value is not None]
upper_bound, lower_bound = Plot.find_outliers(values)
for sample in self.sample_list:
if sample.value:
if upper_bound and sample.value > upper_bound:
sample.outlier = True
elif lower_bound and sample.value < lower_bound:
sample.outlier = True
else:
sample.outlier = False
def get_attributes(self):
"""Finds which extra attributes apply to this dataset"""
# Get attribute names and distinct values for each attribute
results = g.db.execute('''
SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRefNew.Value
FROM CaseAttribute, CaseAttributeXRefNew
WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
AND CaseAttributeXRefNew.InbredSetId = %s
ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
self.attributes = {}
for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
key, name = attr
self.attributes[key] = Bunch()
self.attributes[key].name = name
self.attributes[key].distinct_values = [
item.Value for item in values]
self.attributes[key].distinct_values=natural_sort(self.attributes[key].distinct_values)
all_numbers = True
for value in self.attributes[key].distinct_values:
try:
val_as_float = float(value)
except:
all_numbers = False
if all_numbers:
self.attributes[key].alignment = "right"
else:
self.attributes[key].alignment = "left"
def get_extra_attribute_values(self):
if self.attributes:
query = '''
SELECT Strain.Name AS SampleName, CaseAttributeId AS Id, CaseAttributeXRefNew.Value
FROM Strain, StrainXRef, InbredSet, CaseAttributeXRefNew
WHERE StrainXRef.StrainId = Strain.Id
AND InbredSet.Id = StrainXRef.InbredSetId
AND CaseAttributeXRefNew.StrainId = Strain.Id
AND InbredSet.Id = CaseAttributeXRefNew.InbredSetId
AND CaseAttributeXRefNew.InbredSetId = %s
ORDER BY SampleName''' % self.dataset.group.id
results = g.db.execute(query)
for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName):
attribute_values = {}
for item in items:
attribute_value = item.Value
# ZS: If it's an int, turn it into one for sorting
# (for example, 101 would be lower than 80 if
# they're strings instead of ints)
try:
attribute_value = int(attribute_value)
except ValueError:
pass
attribute_values[self.attributes[item.Id].name.lower()] = attribute_value
self.sample_attribute_values[sample_name] = attribute_values
def get_first_attr_col(self):
first_attr_col = 4
if self.se_exists:
first_attr_col += 2
if self.num_cases_exists:
first_attr_col += 1
return first_attr_col
def natural_sort(a_list, key=lambda s: s):
"""
Sort the list into natural alphanumeric order.
"""
def get_alphanum_key_func(key):
def convert(text): return int(text) if text.isdigit() else text
return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))]
sort_key = get_alphanum_key_func(key)
sorted_list = sorted(a_list, key=sort_key)
return sorted_list
|
