From 34fefed3ed8ac2ef4382934518ea448963aeaad2 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Thu, 6 May 2021 20:35:31 +0200
Subject: [PATCH] Add literate programming notebook

---
 docs/experiments.org | 72 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 docs/experiments.org

diff --git a/docs/experiments.org b/docs/experiments.org
new file mode 100644
index 0000000..edad193
--- /dev/null
+++ b/docs/experiments.org
@@ -0,0 +1,72 @@
+#+TITLE: Tensorflow experiments
+#+AUTHOR: Amin Kasrou Aouam
+#+PROPERTY: header-args :session poetry-session
+* Experiments
+
+#+begin_src elisp :results silent
+(pyvenv-activate "~/.cache/pypoetry/virtualenvs/locimend-hM_4JND0-py3.8/")
+#+end_src
+
+In this notebook we'll extract knowledge from our generated dataset. First, let's import our dependencies:
+
+#+begin_src python
+from tensorflow_io import genome
+#+end_src
+
+#+RESULTS:
+: 2021-05-06 20:41:53.592058: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /nix/store/9ilyrqidrjbqvmnn8ykjc7lygdd86g7q-gcc-10.2.0-lib/lib:
+: 2021-05-06 20:41:53.592101: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
+
+
+Tensorflow I/O is an extension that contains a module for genome parsing, we'll use it to import the sequences contained in our FASTQ files:
+
+#+begin_src python :results silent
+def parse_data(filepath):
+    HVR = genome.read_fastq(filename=filepath)
+    return HVR.sequences, HVR.raw_quality
+#+end_src
+
+Let's import both the immuneSIM generated HVR dataset and the CuReSim processed one, which contains sequencing errors (mostly indels):
+
+#+begin_src python
+original_HVR, _ = parse_data("../data/HVR.fastq")
+processed_HVR, _ = parse_data("../data/CuReSim-HVR.fastq")
+print(original_HVR)
+print(processed_HVR)
+#+end_src
+
+#+RESULTS:
+#+begin_example
+tf.Tensor(
+[b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'
+ b'TGTGCCAGCAGCTTAACCATCGGACGCAGTACTTCGGGCCAGGCACGCGGCTCCTGG'], shape=(10,), dtype=string)
+tf.Tensor(
+[b'GCGCCAGCAGCTATTGGATATGGACTAGCTACTC'
+ b'TGTGCCAGCAGTGATGTGGTGACATGGGTGCGTAGCAATCAGCCAGCATG'
+ b'GCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGTGACAGGGTGCGTAGCATCAGCCCCAGCATTT'
+ b'TTGCGCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TTGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCAGCATTT'
+ b'TTGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'
+ b'TGCGCCAGCAGCTTGGATAGGACTAGCTACTT'
+ b'TGTGCCAGCAGTGAATGGGGACAGGGGCGTAGCAATCAGCCCCAGCATTT'], shape=(20,), dtype=string)
+#+end_example