import re import itertools from gn2.wqflask.database import database_connection from gn2.base import webqtlCaseData, webqtlConfig from pprint import pformat as pf from gn2.utility import Plot from gn2.utility import Bunch from gn2.utility.tools import get_setting class SampleList: 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_", "") # 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: # 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) # 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, {}) # Add a url so RRID case attributes can be displayed as links if '36' in sample.extra_attributes: rrid_string = str(sample.extra_attributes['36']) if self.dataset.group.species == "mouse": if len(rrid_string.split(":")) > 1: the_rrid = rrid_string.split(":")[1] sample.extra_attributes['36'] = [ rrid_string] sample.extra_attributes['36'].append( webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": # Check if it's a list just in case a parent/f1 strain also shows up in the .geno file, to avoid being added twice if len(rrid_string) and not isinstance(sample.extra_attributes['36'], list): the_rrid = rrid_string.split("_")[1] sample.extra_attributes['36'] = [ rrid_string] sample.extra_attributes['36'].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 = False if (any(sample.num_cases for sample in self.sample_list) and any((sample.num_cases and sample.num_cases != "1") for sample in self.sample_list)): self.num_cases_exists = True 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 " --> %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 with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute( "SELECT DISTINCT CaseAttribute.CaseAttributeId, " "CaseAttribute.Name, CaseAttribute.Description, " "CaseAttributeXRefNew.Value FROM " "CaseAttribute, CaseAttributeXRefNew WHERE " "CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.CaseAttributeId " "AND CaseAttributeXRefNew.InbredSetId = %s " "AND CaseAttribute.InbredSetId = %s " "ORDER BY CaseAttribute.CaseAttributeId", (str(self.dataset.group.id),str(self.dataset.group.id)) ) self.attributes = {} for attr, values in itertools.groupby( cursor.fetchall(), lambda row: (row[0], row[1], row[2]) ): key, name, description = attr self.attributes[key] = Bunch() self.attributes[key].id = key self.attributes[key].name = name self.attributes[key].description = description self.attributes[key].distinct_values = [ item[3] 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 break if all_numbers: self.attributes[key].alignment = "right" else: self.attributes[key].alignment = "left" def get_extra_attribute_values(self): if self.attributes: with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute( "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,) ) for sample_name, items in itertools.groupby( cursor.fetchall(), lambda row: row[0] ): attribute_values = {} # Make a list of attr IDs without values (that have values for other samples) valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()] for item in items: sample_name, _id, value = item valueless_attr_ids.remove(_id) attribute_value = value # 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[str(_id)] = attribute_value for attr_id in valueless_attr_ids: attribute_values[str(attr_id)] = "" 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