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lanl · May 8, 2024 · 44641aa · 44641aa
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diff --git a/docs/_sources/index.rst b/docs/_sources/index.rst
@@ -75,10 +75,10 @@ The 'data_preprocessing' directory holds all the data generation steps and divid
      - Scripts
    * - Download human genome assembly (GRCh37/hg19) and `uniform TFBS <https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2215774794_SHfvFO0XVRMcn6xaqOTugAa1Faf1&c=chr1&g=wgEncodeAwgTfbsUniform>`_
      - ``0_download_data.py``
-   * -
-     -
-   * -
-     -
+   * - Preprocess TFBS narrowpeak files and human genome
+     - ``1_preprocess_narrowPeaks_and_humanGenome.sh``
+   * - Overlapping computation for label association
+     - ``2.1_compute_overlappings_job.sh``<br /> ``2.2_compute_overlappings.sh``<br /> ``3_postprocess.sh``
    * -
      -
    * -
@@ -89,8 +89,8 @@ The 'data_preprocessing' directory holds all the data generation steps and divid
      -
 
 .. |   | ``````  |
-.. | Preprocess TFBS narrowpeak files and human genome | ```1_preprocess_narrowPeaks_and_humanGenome.sh``` |
-.. | Overlapping computation for label association | ```2.1_compute_overlappings_job.sh```<br /> ```2.2_compute_overlappings.sh```<br /> ```3_postprocess.sh``` |
+.. |  | ````` |
+.. |  |  |
 .. | Label association | ```5.1_extract_bins_containingOtherThanACGT.ipynb```<br /> ```5.2_compute_peaks_with_labels_clean.sh```|
 .. | Data preprocessing for DNA breathing dynamics generation and DNABERT2 | ```6.1_create_data_for_pydnaepbd.ipynb```<br />  ```6.2_create_data_for_dnabert2.ipynb``` |
 .. | Train/validation/test split| ```7_create_train_val_test_set.ipynb``` |

diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/index.html b/docs/index.html
@@ -409,11 +409,11 @@ <h1>Data Preprocessing Steps<a class="headerlink" href="#data-preprocessing-step
 <tr class="row-even"><td><p>Download human genome assembly (GRCh37/hg19) and <a class="reference external" href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2215774794_SHfvFO0XVRMcn6xaqOTugAa1Faf1&amp;c=chr1&amp;g=wgEncodeAwgTfbsUniform">uniform TFBS</a></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">0_download_data.py</span></code></p></td>
 </tr>
-<tr class="row-odd"><td></td>
-<td></td>
+<tr class="row-odd"><td><p>Preprocess TFBS narrowpeak files and human genome</p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">1_preprocess_narrowPeaks_and_humanGenome.sh</span></code></p></td>
 </tr>
-<tr class="row-even"><td></td>
-<td></td>
+<tr class="row-even"><td><p>Overlapping computation for label association</p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">2.1_compute_overlappings_job.sh``&lt;br</span> <span class="pre">/&gt;</span> <span class="pre">``2.2_compute_overlappings.sh``&lt;br</span> <span class="pre">/&gt;</span> <span class="pre">``3_postprocess.sh</span></code></p></td>
 </tr>
 <tr class="row-odd"><td></td>
 <td></td>

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs_builder/source/index.rst b/docs_builder/source/index.rst
@@ -75,10 +75,10 @@ The 'data_preprocessing' directory holds all the data generation steps and divid
      - Scripts
    * - Download human genome assembly (GRCh37/hg19) and `uniform TFBS <https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2215774794_SHfvFO0XVRMcn6xaqOTugAa1Faf1&c=chr1&g=wgEncodeAwgTfbsUniform>`_
      - ``0_download_data.py``
-   * -
-     -
-   * -
-     -
+   * - Preprocess TFBS narrowpeak files and human genome
+     - ``1_preprocess_narrowPeaks_and_humanGenome.sh``
+   * - Overlapping computation for label association
+     - ``2.1_compute_overlappings_job.sh``<br /> ``2.2_compute_overlappings.sh``<br /> ``3_postprocess.sh``
    * -
      -
    * -
@@ -89,8 +89,8 @@ The 'data_preprocessing' directory holds all the data generation steps and divid
      -
 
 .. |   | ``````  |
-.. | Preprocess TFBS narrowpeak files and human genome | ```1_preprocess_narrowPeaks_and_humanGenome.sh``` |
-.. | Overlapping computation for label association | ```2.1_compute_overlappings_job.sh```<br /> ```2.2_compute_overlappings.sh```<br /> ```3_postprocess.sh``` |
+.. |  | ````` |
+.. |  |  |
 .. | Label association | ```5.1_extract_bins_containingOtherThanACGT.ipynb```<br /> ```5.2_compute_peaks_with_labels_clean.sh```|
 .. | Data preprocessing for DNA breathing dynamics generation and DNABERT2 | ```6.1_create_data_for_pydnaepbd.ipynb```<br />  ```6.2_create_data_for_dnabert2.ipynb``` |
 .. | Train/validation/test split| ```7_create_train_val_test_set.ipynb``` |