Add literate programming notebook

docs/experiments.org

@@ -14,8 +14,8 @@ 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 20:19:46.143707: 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.
+: 2021-05-06 20:19:46.143750: 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:
@@ -29,44 +29,7 @@ def parse_data(filepath):
 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")
+original_HVR, _ = parse_data("data/HVR.fastq")
-processed_HVR, _ = parse_data("../data/CuReSim-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