Merge pull request #1285 from deeptools/ESS

effective genome sizes in docs
deeptools · Jan 10, 2024 · 5790f38 · 5790f38
2 parents d027314 + 9dd5c03
commit 5790f38
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -63,9 +63,9 @@ jobs:
         micromamba activate test_and_build
         rm -f dist/*
         python -m build
-    - uses: actions/upload-artifact@master
+    - uses: actions/upload-artifact@v3
       with:
-        name: "Dist files"
+        name: "distfiles"
         path: "dist"
   test-wheels:
     name: test wheel
@@ -78,7 +78,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/download-artifact@v3
         with:
-          name: "Dist files"
+          name: "distfiles"
           path: ~/dist/
       - uses: actions/setup-python@v4
         with:

diff --git a/CHANGES.txt b/CHANGES.txt
@@ -3,6 +3,8 @@
 * doc fixes (argparse properly displayed, minor changes in installation instructions)
 * deepblue support stops
 * initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better).
+* documentation changes to improve ESS tab, table constraints have been lifted & sphinx_rtd_theme to v2.0.0
+* upload artifact in gh test runner pinned to 3
 
 3.5.4
 * error handling and cases for bwAverage with >2 samples

diff --git a/docs/_static/fix_tables.css b/docs/_static/fix_tables.css
diff --git a/docs/content/feature/effectiveGenomeSize.rst b/docs/content/feature/effectiveGenomeSize.rst
@@ -6,30 +6,56 @@ A number of tools can accept an "effective genome size". This is defined as the
   1. The number of non-N bases in the genome.
   2. The number of regions (of some size) in the genome that are uniquely mappable (possibly given some maximal edit distance).
 
-Option 1 can be computed using ``faCount`` from `Kent's tools <http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>`__. The effective genome size for a number of genomes using this method is given below:
-
-======== ==============
-Genome   Effective size
-======== ==============
-GRCh37   2864785220
-GRCh38   2913022398
-GRCm37   2620345972
-GRCm38   2652783500
-dm3      162367812
-dm6      142573017
-GRCz10   1369631918
-WBcel235 100286401
-TAIR10   119481543 
-======== ==============
-
-These values only appropriate if multimapping reads are included. If they are excluded (or there's any MAPQ filter applied), then values derived from option 2 are more appropriate. These are then based on the read length. We can approximate these values for various read lengths using the `khmer program <http://khmer.readthedocs.io/en/v2.1.1/>`__ program and ``unique-kmers.py`` in particular. A table of effective genome sizes given a read length using this method is provided below:
-
-=========== ========== ========== ========== ========== ========= ========= ========== ========
-Read length GRCh37     GRCh38     GRCm37     GRCm38     dm3       dm6       GRCz10     WBcel235
-=========== ========== ========== ========== ========== ========= ========= ========== ========
-50          2685511504 2701495761 2304947926 2308125349 130428560 125464728 1195445591 95159452
-75          2736124973 2747877777 2404646224 2407883318 135004462 127324632 1251132686 96945445
-100         2776919808 2805636331 2462481010 2467481108 139647232 129789873 1280189044 98259998
-150         2827437033 2862010578 2489384235 2494787188 144307808 129941135 1312207169 98721253
-200         2855464000 2887553303 2513019276 2520869189 148524010 132509163 1321355241 98672758
-=========== ========== ========== ========== ========== ========= ========= ========== ========
+Option 1 can be computed using ``faCount`` from `Kents tools  <https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>`__. 
+The effective genome size for a number of genomes using this method is given below:
+
+
++---------------+------------------+
+| Genome        | Effective size   |
++===============+==================+
+|GRCh37         |    2864785220    |
++---------------+------------------+
+|GRCh38         |    2913022398    |
++---------------+------------------+
+|T2T/CHM13CAT_v2|    3117292070    |
++---------------+------------------+
+|GRCm37         |    2620345972    |
++---------------+------------------+
+|GRCm38         |    2652783500    |
++---------------+------------------+
+|dm3            |    162367812     |
++---------------+------------------+
+|dm6            |    142573017     |
++---------------+------------------+
+|GRCz10         |    1369631918    |
++---------------+------------------+
+|GRCz11         |    1368780147    |
++---------------+------------------+
+|WBcel235       |    100286401     |
++---------------+------------------+
+|TAIR10         |    119482012     |
++---------------+------------------+
+
+
+
+These values only appropriate if multimapping reads are included. If they are excluded (or there's any MAPQ filter applied), 
+then values derived from option 2 are more appropriate. 
+These are then based on the read length. 
+We can approximate these values for various read lengths using the `khmer program <https://khmer.readthedocs.io/en/latest/>`__ program and ``unique-kmers.py`` in particular.
+A table of effective genome sizes given a read length using this method is provided below:
+
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|Read length      | GRCh37          | GRCh38          | T2T/CHM13CAT_v2 | GRCm37          | GRCm38          | dm3             | dm6             | GRCz10          | GRCz11          | WBcel235        | TAIR10          |
++=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
+|50               | 2685511454      | 2701495711      | 2725240337      | 2304947876      | 2308125299      | 130428510       | 125464678       | 1195445541      | 1197575653      | 95159402        | 114339094       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|75               | 2736124898      | 2747877702      | 2786136059      | 2404646149      | 2407883243      | 135004387       | 127324557       | 1251132611      | 1250812288      | 96945370        | 115317469       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|100              | 2776919708      | 2805636231      | 2814334875      | 2462480910      | 2467481008      | 139647132       | 129789773       | 1280188944      | 1280354977      | 98259898        | 118459858       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|150              | 2827436883      | 2862010428      | 2931551487      | 2489384085      | 2494787038      | 144307658       | 129940985       | 1312207019      | 1311832909      | 98721103        | 118504138       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|200              | 2855463800      | 2887553103      | 2936403235      | 2513019076      | 2520868989      | 148523810       | 132508963       | 1321355041      | 1322366338      | 98672558        | 117723393       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|250              | 2855044784      | 2898802627      | 2960856300      | 2528988583      | 2538590322      | 151901455       | 132900923       | 1339205109      | 1342093482      | 101271756       | 119585546       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,4 @@
 sphinx==7.2.6
 mock==5.1.0
-sphinx_rtd_theme==1.3.0
+sphinx_rtd_theme==2.0.0
 sphinx-argparse==0.4.0
diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -1,3 +1,3 @@
 {% extends "!layout.html" %}
 {% set script_files = script_files + ["_static/welcome_owl.carousel.min.js"] %}
-{% set css_files = css_files + ["_static/welcome_owl.carousel.css", "_static/welcome_owl.carousel.theme.css", "_static/fix_tables.css"] %}
+{% set css_files = css_files + ["_static/welcome_owl.carousel.css", "_static/welcome_owl.carousel.theme.css"] %}