diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 70 |
1 files changed, 35 insertions, 35 deletions
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index b43b57dc..dccd1ba8 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,83 +1,82 @@ import re -from flask import Flask, g +import itertools +import utility.logger +from flask import g from base import webqtlCaseData -from utility import webqtlUtil, Plot, Bunch -from base.trait import GeneralTrait -import numpy as np -from scipy import stats -from pprint import pformat as pf +from utility import Plot +from utility import Bunch -import simplejson as json +from pprint import pformat as pf -import itertools +logger = utility.logger.getLogger(__name__) -import utility.logger -logger = utility.logger.getLogger(__name__ ) class SampleList(object): def __init__(self, dataset, sample_names, this_trait, - sample_group_type = "primary", - header = "Samples"): + 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_list = [] # The actual list self.sample_attribute_values = {} self.get_attributes() - #self.sample_qnorm = get_transform_vals(self.dataset, this_trait) - 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_", "") - if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait - if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X': - sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1])) + # ZS: self.this_trait will be a list if it is a Temp trait + if isinstance(self.this_trait, list): + if (counter <= len(self.this_trait) and + str(self.this_trait[counter-1]).upper() != 'X'): + sample = webqtlCaseData.webqtlCaseData( + name=sample_name, + value=float(self.this_trait[counter-1])) else: sample = webqtlCaseData.webqtlCaseData(name=sample_name) 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) + # 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: - #logger.debug("No sample %s, let's create it now" % sample_name) 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'): + 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) - #### For extra attribute columns; currently only used by several datasets - Zach + # For extra attribute columns; currently only used by + # several datasets - Zach if self.sample_attribute_values: - sample.extra_attributes = self.sample_attribute_values.get(sample_name, {}) - #logger.debug("sample.extra_attributes is", pf(sample.extra_attributes)) - + sample.extra_attributes = self.sample_attribute_values.get( + sample_name, {}) self.sample_list.append(sample) - - #logger.debug("attribute vals are", pf(self.sample_attribute_values)) - 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 != None] + 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: @@ -105,7 +104,8 @@ class SampleList(object): 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 = [ + item.Value for item in values] natural_sort(self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: @@ -138,8 +138,9 @@ class SampleList(object): 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) + # 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: @@ -154,13 +155,12 @@ class SampleList(object): return any(sample.variance for sample in self.sample_list) -def natural_sort(list, key=lambda s:s): +def natural_sort(list, key=lambda s: s): """ Sort the list into natural alphanumeric order. """ def get_alphanum_key_func(key): - convert = lambda text: int(text) if text.isdigit() else text + 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) list.sort(key=sort_key) - |