Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 117 insertions, 0 deletions

diff --git a/wqflask/base/species.py b/wqflask/base/species.py
new file mode 100644
index 00000000..9d4cac4c
--- /dev/null
+++ b/wqflask/base/species.py
@@ -0,0 +1,117 @@
+from __future__ import absolute_import, print_function, division
+
+import collections
+
+from flask import Flask, g
+
+#from MySQLdb import escape_string as escape
+
+from utility import Bunch
+
+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)
+        self.genome_mb_length = self.chromosomes.get_genome_mb_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))
+    #            
+    #    print("chromosomes is: ", pf(chromosomes))       
+    #            
+    #    return chromosomes
+
+class IndChromosome(object):
+    def __init__(self, length):
+        self.length = length
+        
+    @property
+    def mb_length(self):
+        """Chromosome length in megabases"""
+        return self.length / 1000000
+    
+    def set_cm_length(self, genofile_chr):
+        self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
+
+
+class Chromosomes(object):
+    def __init__(self, dataset):
+        self.dataset = dataset
+        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
+                """, self.dataset.group.name).fetchall()
+        print("bike:", results)
+
+        for item in results:
+            self.chromosomes[item.Name] = IndChromosome(item.Length)
+        
+        self.set_mb_graph_interval()
+        self.get_cm_length_list()
+
+
+    def set_mb_graph_interval(self):
+        """Empirical megabase interval"""
+        
+        #if self.chromosomes:
+        assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+        self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        #else:
+            #self.mb_graph_interval = 1
+
+
+    def get_genome_mb_length(self):
+        """Gets the sum of each chromosome's length in megabases"""
+
+        return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
+
+
+    def get_genome_cm_length(self):
+        """Gets the sum of each chromosome's length in centimorgans"""
+
+        return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
+
+    def get_cm_length_list(self):
+        """Chromosome length in centimorgans
+        
+        Calculates the length in centimorgans by subtracting the centimorgan position
+        of the last marker in a chromosome by the position of the first marker
+        
+        """
+        
+        self.dataset.group.read_genotype_file()
+        
+        self.cm_length_list = []
+        
+        for chromosome in self.dataset.group.genotype:
+            self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
+            
+        print("self.cm_length_list:", pf(self.cm_length_list))
+        
+        assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
+        for counter, chromosome in enumerate(self.chromosomes.values()):
+            chromosome.cm_length = self.cm_length_list[counter]
+            #self.chromosomes[counter].cm_length = item
+            
+        for key, value in self.chromosomes.items():
+            print("bread - %s: %s" % (key, pf(vars(value))))
+        
+
+# Testing                
+#if __name__ == '__main__':    
+#    foo = dict(bar=dict(length))
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