From 56ce88ad31dec3cece63e9370ca4e4c02139753b Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Tue, 16 Mar 2021 11:38:13 +0300 Subject: 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 * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz --- gn3/utility/species.py | 71 -------------------------------------------------- 1 file changed, 71 deletions(-) delete mode 100644 gn3/utility/species.py (limited to 'gn3/utility/species.py') 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) -- cgit v1.2.3