diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 6 | ||||
| -rw-r--r-- | wqflask/base/species.py | 52 |
2 files changed, 45 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 36d4acaf..50ef8f57 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -85,8 +85,8 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.allsamples = None - - + + #def read_genotype(self): # self.read_genotype_file() # @@ -158,8 +158,8 @@ class DataSet(object): self.retrieve_other_names() - self.species = species.TheSpecies(self) self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + self.species = species.TheSpecies(self) diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 98941ce5..1fd76772 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -1,16 +1,48 @@ -from __future__ import print_function, division +from __future__ import absolute_import, print_function, division +import collections + +from flask import Flask, g + +#from MySQLdb import escape_string as escape + +from pprint import pformat as pf class TheSpecies(object): def __init__(self, dataset): self.dataset = dataset + print("self.dataset is:", pf(self.dataset.__dict__)) + self.chromosomes = Chromosomes(self.dataset.group.name) + + #@property + #def chromosomes(self): + # chromosomes = [("All", -1)] + # + # for counter, genotype in enumerate(self.dataset.group.genotype): + # if len(genotype) > 1: + # chromosomes.append((genotype.name, counter)) + # + # print("chromosomes is: ", pf(chromosomes)) + # + # return chromosomes + + + +class Chromosomes(object): + def __init__(self, group_name): + self.chromosomes = collections.OrderedDict() + + results = g.db.execute(""" + Select + Chr_Length.Name, Length from Chr_Length, InbredSet + where + Chr_Length.SpeciesId = InbredSet.SpeciesId AND + InbredSet.Name = %s + Order by OrderId + """, group_name).fetchall() + print("bike:", results) + + for item in results: + self.chromosomes[item.Name] = item.Length - @property - def chromosomes(self): - chromosomes = [("All", -1)] - - for counter, genotype in enumerate(self.dataset.group.genotype): - if len(genotype) > 1: - chromosomes.append((genotype.name, counter)) - - return chromosomes + print("self.chromosomes:", self.chromosomes) |