Merge pull request #38 from MannLabs/go_analysis

Go analysis

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.2
+current_version = 0.2.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.9"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: docs/requirements_docs.txt

HISTORY.md

@@ -16,3 +16,5 @@
 * rawdata renamed to rawinput
 * GUI bug fix
 
+## 0.2.0
+* Gene Ontology Enrichment Analysis using a GO tool

alphastats/DataSet.py

@@ -17,6 +17,7 @@
 
 from alphastats.DataSet_Plot import Plot
 from alphastats.DataSet_Preprocess import Preprocess
+from alphastats.DataSet_Pathway import Enrichment
 from alphastats.DataSet_Statistics import Statistics
 from alphastats.utils import LoaderError
 
@@ -25,7 +26,7 @@
 warnings.filterwarnings("ignore", category=UserWarning, module="openpyxl")
 
 
-class DataSet(Preprocess, Statistics, Plot):
+class DataSet(Preprocess, Statistics, Plot, Enrichment):
     """Analysis Object
     """
 
@@ -46,6 +47,7 @@ def __init__(self, loader, metadata_path=None, sample_column=None):
         self.index_column = loader.index_column
         self.intensity_column = loader.intensity_column
         self.filter_columns = loader.filter_columns
+        self.evidence_df = loader.evidence_df
         self.gene_names = loader.gene_names
 
         # include filtering before