1 files changed, 71 insertions, 0 deletions
diff --git a/gn3/utility/species.py b/gn3/utility/species.py
new file mode 100644
index 0000000..0140d41
--- /dev/null
+++ b/gn3/utility/species.py
@@ -0,0 +1,71 @@
+"""module contains species and chromosomes classes"""
+import collections
+
+from flask import g
+
+
+from gn3.utility.logger import getLogger
+logger = getLogger(__name__)
+
+ # pylint: disable=too-few-public-methods
+ # intentionally disabled check for few public methods
+
+class TheSpecies:
+    """class for Species"""
+
+    def __init__(self, dataset=None, species_name=None):
+        if species_name is not None:
+            self.name = species_name
+            self.chromosomes = Chromosomes(species=self.name)
+        else:
+            self.dataset = dataset
+            self.chromosomes = Chromosomes(dataset=self.dataset)
+
+
+
+class IndChromosome:
+    """class for IndChromosome"""
+
+    def __init__(self, name, length):
+        self.name = name
+        self.length = length
+
+    @property
+    def mb_length(self):
+        """Chromosome length in megabases"""
+        return self.length / 1000000
+
+
+
+
+class Chromosomes:
+    """class for Chromosomes"""
+
+    def __init__(self, dataset=None, species=None):
+        self.chromosomes = collections.OrderedDict()
+        if species is not None:
+            query = """
+                Select
+                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
+                where
+                        Chr_Length.SpeciesId = Species.SpeciesId AND
+                        Species.Name = '%s'
+                Order by OrderId
+                """ % species.capitalize()
+        else:
+            self.dataset = dataset
+
+            query = """
+                Select
+                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
+                where
+                        Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+                        InbredSet.Name = '%s'
+                Order by OrderId
+                """ % self.dataset.group.name
+        logger.sql(query)
+        results = g.db.execute(query).fetchall()
+
+        for item in results:
+            self.chromosomes[item.OrderId] = IndChromosome(
+                item.Name, item.Length)