From c8a4719a83e3ee65a8c03b0b600a3cfea9ff17bf Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 8 Jan 2013 14:46:07 -0600
Subject: Deleted some unnecessary code in marker_regression.py and fixed some
 bugs

Added a couple utility functions to the Chromosomes class in species.py
---
 wqflask/base/species.py | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

(limited to 'wqflask/base/species.py')

diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 1fd76772..85f076ca 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -13,7 +13,8 @@ class TheSpecies(object):
         self.dataset = dataset
         print("self.dataset is:", pf(self.dataset.__dict__))
         self.chromosomes = Chromosomes(self.dataset.group.name)
-
+        self.genome_length = self.chromosomes.get_genome_length()
+        
     #@property
     #def chromosomes(self):
     #    chromosomes = [("All", -1)]
@@ -31,7 +32,7 @@ class TheSpecies(object):
 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
@@ -46,3 +47,20 @@ class Chromosomes(object):
             self.chromosomes[item.Name] = item.Length
 
         print("self.chromosomes:", self.chromosomes)
+
+
+    def get_mb_length(self):
+        """Gets the chromosome length in megabases"""
+
+        mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes
+
+        return mb_lengths
+
+    def get_genome_length(self):
+        """Gets the sum of each chromosome's length"""
+
+        genome_length = 0
+        for name, value in self.chromosomes.items():
+            genome_length += value
+
+        return genome_length
\ No newline at end of file
-- 
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