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import re
import itertools
from flask import g
from base import webqtlCaseData, webqtlConfig
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, {})
#ZS: Add a url so RRID case attributes can be displayed as links
if 'rrid' in sample.extra_attributes:
if self.dataset.group.species == "mouse":
if len(sample.extra_attributes['rrid'].split(":")) > 1:
the_rrid = sample.extra_attributes['rrid'].split(":")[1]
sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']]
sample.extra_attributes['rrid'].append(webqtlConfig.RRID_MOUSE_URL % the_rrid)
elif self.dataset.group.species == "rat":
if len(str(sample.extra_attributes['rrid'])):
the_rrid = sample.extra_attributes['rrid'].split("_")[1]
sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']]
sample.extra_attributes['rrid'].append(webqtlConfig.RRID_RAT_URL % the_rrid)
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
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