1 files changed, 59 insertions, 0 deletions
diff --git a/gn2/base/species.py b/gn2/base/species.py
new file mode 100644
index 00000000..0844fada
--- /dev/null
+++ b/gn2/base/species.py
@@ -0,0 +1,59 @@
+from dataclasses import dataclass
+from typing import Optional, Union
+from collections import OrderedDict
+
+
+class TheSpecies:
+    """Data related to species."""
+
+    def __init__(self, dataset=None, species_name=None) -> None:
+        "Initialise the Species object"
+        self.dataset = dataset
+        self.name = self.species_name = species_name
+        self.chromosomes = Chromosomes(species=species_name,
+                                       dataset=dataset)
+
+
+@dataclass
+class IndChromosome:
+    """Data related to IndChromosome"""
+    name: str
+    length: int
+
+    @property
+    def mb_length(self) -> Union[int, float]:
+        """Chromosome length in mega-bases"""
+        return self.length / 1000000
+
+
+@dataclass
+class Chromosomes:
+    """Data related to a chromosome"""
+
+    def __init__(self, dataset, species: Optional[str]) -> None:
+        "initialise the Chromosome object"
+        self.species = species
+        if species is None:
+            self.dataset = dataset
+
+    def chromosomes(self, db_cursor) -> OrderedDict:
+        """Lazily fetch the chromosomes"""
+        chromosomes = OrderedDict()
+        if self.species is not None:
+            db_cursor.execute(
+                "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", (self.species.capitalize(),))
+        else:
+            db_cursor.execute(
+                "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,))
+        for name, _, length in db_cursor.fetchall():
+            chromosomes[name] = IndChromosome(
+                name=name, length=length)
+        return chromosomes