rerun pipeline to update results

dms-vep · Dec 12, 2023 · be1ba10 · be1ba10
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diff --git a/data/.DS_Store b/data/.DS_Store
diff --git a/docs/150C_escape_plot.html b/docs/150C_escape_plot.html
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diff --git a/docs/4299_escape_plot.html b/docs/4299_escape_plot.html
diff --git a/docs/4584_escape_plot.html b/docs/4584_escape_plot.html
diff --git a/docs/68C_escape_plot.html b/docs/68C_escape_plot.html
diff --git a/docs/74C_escape_plot.html b/docs/74C_escape_plot.html
diff --git a/docs/AUSAB-05_escape_plot.html b/docs/AUSAB-05_escape_plot.html
diff --git a/docs/AUSAB-08_escape_plot.html b/docs/AUSAB-08_escape_plot.html
diff --git a/docs/AUSAB-13_escape_plot.html b/docs/AUSAB-13_escape_plot.html
diff --git a/docs/AUSAB-16_escape_plot.html b/docs/AUSAB-16_escape_plot.html
diff --git a/docs/_images/analyze_func_scores_20_0.png b/docs/_images/analyze_func_scores_20_0.png
diff --git a/docs/_sources/avg_antibody_escape.rst.txt b/docs/_sources/avg_antibody_escape.rst.txt
@@ -33,10 +33,4 @@ Antibody-escape averaged across replicates
 - :doc:`68C <avg_antibody_escape_68C>`
 - :doc:`150C <avg_antibody_escape_150C>`
 - :doc:`18C <avg_antibody_escape_18C>`
-- :doc:`ferret_2 <avg_antibody_escape_ferret_2>`
-- :doc:`AUSAB-05 <avg_antibody_escape_AUSAB-05>`
-- :doc:`AUSAB-08 <avg_antibody_escape_AUSAB-08>`
-- :doc:`AUSAB-16 <avg_antibody_escape_AUSAB-16>`
-- :doc:`ferret_1 <avg_antibody_escape_ferret_1>`
-- :doc:`ferret_3 <avg_antibody_escape_ferret_3>`
 
diff --git a/docs/_sources/fit_globalepistasis.rst.txt b/docs/_sources/fit_globalepistasis.rst.txt
@@ -9,7 +9,6 @@ Fit global epistasis models
 - :doc:`libA_220303_1_plasmid_1_vs_230403_1_no-antibody_control_1 <fit_globalepistasis_libA_220303_1_plasmid_1_vs_230403_1_no-antibody_control_1>`
 - :doc:`libA_220303_1_plasmid_1_vs_230419_1_no-antibody_control_1 <fit_globalepistasis_libA_220303_1_plasmid_1_vs_230419_1_no-antibody_control_1>`
 - :doc:`libA_220303_1_plasmid_1_vs_230425_1_no-antibody_control_1 <fit_globalepistasis_libA_220303_1_plasmid_1_vs_230425_1_no-antibody_control_1>`
-- :doc:`libA_220303_1_plasmid_1_vs_230517_1_no-antibody_control_1 <fit_globalepistasis_libA_220303_1_plasmid_1_vs_230517_1_no-antibody_control_1>`
 - :doc:`libA_220303_1_plasmid_1_vs_230620_1_no-antibody_control_1 <fit_globalepistasis_libA_220303_1_plasmid_1_vs_230620_1_no-antibody_control_1>`
 - :doc:`libB_220303_1_plasmid_1_vs_230118_1_no-antibody_control_1 <fit_globalepistasis_libB_220303_1_plasmid_1_vs_230118_1_no-antibody_control_1>`
 - :doc:`libB_220303_1_plasmid_1_vs_230407_1_no-antibody_control_1 <fit_globalepistasis_libB_220303_1_plasmid_1_vs_230407_1_no-antibody_control_1>`

diff --git a/docs/_sources/fit_polyclonal.rst.txt b/docs/_sources/fit_polyclonal.rst.txt
@@ -57,17 +57,11 @@ Fit ``polyclonal`` models
 - :doc:`libB_230502_1_150C_2 <fit_polyclonal_libB_230502_1_150C_2>`
 - :doc:`libB_230502_1_18C_2 <fit_polyclonal_libB_230502_1_18C_2>`
 - :doc:`libB_230502_1_210C_2 <fit_polyclonal_libB_230502_1_210C_2>`
-- :doc:`libA_230517_1_ferret_2_1 <fit_polyclonal_libA_230517_1_ferret_2_1>`
-- :doc:`libA_230517_1_AUSAB-05_2 <fit_polyclonal_libA_230517_1_AUSAB-05_2>`
-- :doc:`libA_230517_1_AUSAB-08_2 <fit_polyclonal_libA_230517_1_AUSAB-08_2>`
-- :doc:`libA_230517_1_AUSAB-16_2 <fit_polyclonal_libA_230517_1_AUSAB-16_2>`
 - :doc:`libA_230620_1_2388_2 <fit_polyclonal_libA_230620_1_2388_2>`
 - :doc:`libA_230620_1_2462_1 <fit_polyclonal_libA_230620_1_2462_1>`
 - :doc:`libA_230620_1_2463_2 <fit_polyclonal_libA_230620_1_2463_2>`
 - :doc:`libA_230620_1_3866_1 <fit_polyclonal_libA_230620_1_3866_1>`
 - :doc:`libA_230620_1_3944_1 <fit_polyclonal_libA_230620_1_3944_1>`
 - :doc:`libA_230620_1_4299_2 <fit_polyclonal_libA_230620_1_4299_2>`
 - :doc:`libA_230620_1_4584_2 <fit_polyclonal_libA_230620_1_4584_2>`
-- :doc:`libA_230620_1_ferret_1_1 <fit_polyclonal_libA_230620_1_ferret_1_1>`
-- :doc:`libA_230620_1_ferret_3_1 <fit_polyclonal_libA_230620_1_ferret_3_1>`
 
diff --git a/docs/_sources/generate_filtered_escape_file.nblink.txt b/docs/_sources/generate_filtered_escape_file.nblink.txt
@@ -0,0 +1,3 @@
+{
+    "path": "../notebooks/generate_filtered_escape_file.ipynb"
+}
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -25,6 +25,7 @@ details, using dropdowns, etc.
    fit_polyclonal
    avg_antibody_escape
    process_perth2009_data
+   generate_filtered_escape_file
 
 Data files
 ----------
@@ -42,6 +43,7 @@ Data files
 - `antibody escape values <https://github.com/dms-vep/flu_h3_hk19_dms/blob/main/./results/antibody_escape>`_
 - `sequential to reference site numbering <https://github.com/dms-vep/flu_h3_hk19_dms/blob/main/./data/site_map.csv>`_
 - `escape for Perth2009 DMS <https://github.com/dms-vep/flu_h3_hk19_dms/blob/main/./results/perth2009/merged_escape.csv>`_
+- `escape for HongKong/2019 DMS <https://github.com/dms-vep/flu_h3_hk19_dms/blob/main/./results/full_hk19_escape_scores.csv>`_
 
 Interactive plots of mutation functional effects
 ------------------------------------------------
@@ -80,11 +82,5 @@ Interactive plots of mutation antibody escape
 - `4584 escape plot <4584_escape_plot.html>`_
 - `68C escape plot <68C_escape_plot.html>`_
 - `74C escape plot <74C_escape_plot.html>`_
-- `AUSAB-05 escape plot <AUSAB-05_escape_plot.html>`_
-- `AUSAB-08 escape plot <AUSAB-08_escape_plot.html>`_
 - `AUSAB-13 escape plot <AUSAB-13_escape_plot.html>`_
-- `AUSAB-16 escape plot <AUSAB-16_escape_plot.html>`_
-- `ferret 1 escape plot <ferret_1_escape_plot.html>`_
-- `ferret 2 escape plot <ferret_2_escape_plot.html>`_
-- `ferret 3 escape plot <ferret_3_escape_plot.html>`_
 
diff --git a/docs/analyze_func_scores.html b/docs/analyze_func_scores.html
diff --git a/docs/analyze_prob_escape.html b/docs/analyze_prob_escape.html
diff --git a/docs/analyze_variant_counts.html b/docs/analyze_variant_counts.html
diff --git a/docs/avg_antibody_escape.html b/docs/avg_antibody_escape.html
@@ -66,12 +66,6 @@ <h1>Antibody-escape averaged across replicates<a class="headerlink" href="#antib
 <li><p><a class="reference internal" href="avg_antibody_escape_68C.html"><span class="doc">68C</span></a></p></li>
 <li><p><a class="reference internal" href="avg_antibody_escape_150C.html"><span class="doc">150C</span></a></p></li>
 <li><p><a class="reference internal" href="avg_antibody_escape_18C.html"><span class="doc">18C</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_ferret_2.html"><span class="doc">ferret_2</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_AUSAB-05.html"><span class="doc">AUSAB-05</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_AUSAB-08.html"><span class="doc">AUSAB-08</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_AUSAB-16.html"><span class="doc">AUSAB-16</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_ferret_1.html"><span class="doc">ferret_1</span></a></p></li>
-<li><p><a class="reference internal" href="avg_antibody_escape_ferret_3.html"><span class="doc">ferret_3</span></a></p></li>
 </ul>
 </section>