diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..d0c3cbf1020d5c292abdedf27627c6abe25e2293
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = source
+BUILDDIR = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..747ffb7b3033659bdd2d1e6eae41ecb00358a45e
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.https://www.sphinx-doc.org/
+ exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/Notizen.md b/docs/source/Notizen.md
similarity index 100%
rename from Notizen.md
rename to docs/source/Notizen.md
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..f305360a75bf69efe043c85d3a799882fc2c4529
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,35 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Autoencoder BigData_Praktikum'
+copyright = '2023, Franziska Roepke, Harpreet Int-Veen, Paul Kühnel'
+author = 'Franziska Roepke, Harpreet Int-Veen, Paul Kühnel'
+release = '0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.todo',
+ 'sphinx.ext.duration',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.viewcode',
+ 'sphinx.ext.autosummary']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', '*.loom', '.DS_Store']
+
+source_suffix = ['.rst', '.md']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
diff --git a/testfiles/how_to_fix_loompy_error.md b/docs/source/how_to_fix_loompy_error.md
similarity index 100%
rename from testfiles/how_to_fix_loompy_error.md
rename to docs/source/how_to_fix_loompy_error.md
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..80a76a3f87d5490948533d3279101855083fa8d8
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,52 @@
+.. Autoencoder BigData_Praktikum documentation master file, created by
+ sphinx-quickstart on Fri May 26 14:36:45 2023.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to Autoencoder BigData_Praktikum's documentation!
+=========================================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+.. note::
+
+ This project is under active development.
+
+
+Development
+===========
+
+Notes
+-----
+
+Some notes during development:
+
+.. toctree::
+
+ Notizen
+
+
+Main documentation
+==================
+
+See API
+
+API
+===
+
+.. autosummary::
+ :toctree: generated
+
+ main_methods
diff --git a/main_methods.py b/main_methods.py
index f51d2929fb55c1a1cf6102e94fc2741e93bfa3b9..3f0ca7942d67e7a992d935c89f5b6daca72a7ff3 100644
--- a/main_methods.py
+++ b/main_methods.py
@@ -1,21 +1,36 @@
import loompy
import pandas as pd
+import os
def loom_to_pandas_df(file_name="testfiles/test.loom"):
"""
- :param file_name: the name of the loom file (default is: "testfiles/test.loom")
+ :param file_name: the name of the loom file (default is:
+ "testfiles/test.loom")
:return: pandas DataFrame
"""
df = pd.DataFrame # Empty DataFrame - to return in case of wrong formatting
-
- if file_name[-4:] != ".loom":
+ if file_name[-5:] != ".loom":
print(f"{file_name} is not a valid file name. Only use '.loom' files!")
with loompy.connect(file_name) as ds:
try:
- df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+ df = pd.DataFrame(data=ds[:, :],
+ index=ds.ra.Gene,
+ columns=ds.ca.input_name)
except AttributeError or ValueError or OSError:
- raise Exception(f"The loom file {file_name} does not exist or has no valid format!")
+ raise Exception(f"The loom file {file_name} does not exist or has "
+ f"no valid format!")
return df
+
+
+print(os.getcwd())
+os.chdir("testfiles")
+print(os.getcwd())
+# print(os.listdir())
+test_df = loom_to_pandas_df("AllelicExpressionPatterns-mouse-brain-SS2.loom")
+test_df.info()
+test_df.describe()
+print(".........")
+print(test_df)
diff --git a/testfiles/loom_test.py b/testfiles/loom_test.py
index 1187d4ba3b133f24d54c46b2df16ee225841fec9..b4e6b07cbef8d4edad2d549a7ad47659d5bfc8a2 100644
--- a/testfiles/loom_test.py
+++ b/testfiles/loom_test.py
@@ -1,9 +1,19 @@
import loompy
import pandas as pd
-ds = loompy.connect("test.loom")
-df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
-ds.close()
+with loompy.connect("AllelicExpressionPatterns-mouse-brain-SS2.loom") as ds:
-df.info()
-df.describe()
\ No newline at end of file
+ #print(ds.ra.Gene)
+ print(ds.ca.input_name)
+ print(ds[0:10, 0:10])
+
+
+
+
+
+#ds = loompy.connect("test.loom")
+#df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+#ds.close()
+
+#df.info()
+#df.describe()