delete unwanted correlation stuff (#5)

* delete unwanted correlation stuff

* Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

* update guix scm file

* fix pylint error for correlations api

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

1 files changed, 0 insertions, 71 deletions

diff --git a/gn3/utility/species.py b/gn3/utility/species.py
deleted file mode 100644
index 0140d41..0000000
--- a/gn3/utility/species.py
+++ /dev/null
@@ -1,71 +0,0 @@
-"""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)