Merge branch 'main' into update-data

Author: hdashnow

.github/workflows/update-loci.yaml

@@ -45,7 +45,7 @@ jobs:
 
       - name: Check loci and update bed files (short)
         if: ${{ github.event_name == 'pull_request'}}
-        run: snakemake --config stages="skip-refs"
+        run: snakemake --cores all --config stages="skip-refs"
 
       # Enable this step to open an SSH session for debugging
       # - name: SSH debug
@@ -57,15 +57,15 @@ jobs:
           conda init
           source /home/runner/.bashrc
           conda activate strchive
-          snakemake --config stages="new-refs"
+          snakemake --cores all --config stages="new-refs"
 
       - name: Update all literature (long)
         if: ${{ github.event_name == 'schedule' }}
         run: |
           conda init
           source /home/runner/.bashrc
           conda activate strchive
-          snakemake
+          snakemake --cores all
 
       - name: Open pull request with updated files
         if: ${{ !(github.event_name == 'pull_request') }}

data/STRchive-loci.json

@@ -32,11 +32,11 @@
   "pathogenic_max": 694.0,
   "ref_copies": 7.7,
   "motif_len": 3,
-  "age_onset": "Typical: 24-30; Range: 10-50 [@pmid:39068203].",
+  "age_onset": "Typical: 24-30; Range: 10-50 [@pmid:39068203]. Age of onset data is limited to 8 families.",
   "age_onset_min": 10,
   "age_onset_max": 50,
-  "typ_age_onset_min": null,
-  "typ_age_onset_max": null,
+  "typ_age_onset_min": 24,
+  "typ_age_onset_max": 30,
   "novel": "ref",
   "mechanism": null,
   "mechanism_detail": "Potentially over-expression of transcripts [@pmid:39068203].",

data/check-loci.txt

@@ -0,0 +1,2 @@
+WARNING: overwriting data/STRchive-loci.json in 5 seconds
+Press Ctrl+C to cancel

data/plots/age-onset.json

@@ -65,7 +65,7 @@
     "type": "bar"
   },
   {
-    "base": [40.0, 50.0, 40.0, 0, 42.0, 50.0, 40.0, 0, 33.0, 0, 0, 43.0, 0, 37.0, 20.0, 30.0, 21.0, 0, 12.0, 0, 0, 30.0, 18.0, 0, 0, 56.0, 26.0, 31.0, 0, 20.0, 0, 12.0, 0, 10.0, 0, 19.0, 30.0, 0, 0, 0, 0, 0, 35.0, 0, 0, 0, 20.0, 4.0, 20.0, 28.0, 0, 10.0, 0, 0.0, 0, 0],
+    "base": [40.0, 50.0, 40.0, 0, 42.0, 50.0, 40.0, 0, 33.0, 0, 0, 43.0, 0, 37.0, 20.0, 30.0, 21.0, 0, 12.0, 24, 0, 30.0, 18.0, 0, 0, 56.0, 26.0, 31.0, 0, 20.0, 0, 12.0, 0, 10.0, 0, 19.0, 30.0, 0, 0, 0, 0, 0, 35.0, 0, 0, 0, 20.0, 4.0, 20.0, 28.0, 0, 10.0, 0, 0.0, 0, 0],
     "hovertemplate": "Disease: %{y} \u003cbr\u003e Typical onset: %{base} - %{x} years",
     "legendgroup": "AD",
     "marker":
@@ -77,7 +77,7 @@
     "orientation": "h",
     "showlegend": false,
     "width": 0.6,
-    "x": [19.0, 10.0, 20.0, 0, 28.0, 14.0, 19.0, 0, 20.0, 0, 0, 9.0, 0, 19.0, 14.0, 22.0, 18.0, 0, 36.0, 0, 0, 40.0, 12.0, 0, 0, 6.0, 24.0, 20.0, 0, 19.0, 0, 18.0, 0, 39.0, 0, 29.0, 9.0, 0, 0, 0, 0, 0, 9.0, 0, 0, 0, 20.0, 44.0, 29.0, 28.0, 0, 20.0, 0, 2.0, 0, 0],
+    "x": [19.0, 10.0, 20.0, 0, 28.0, 14.0, 19.0, 0, 20.0, 0, 0, 9.0, 0, 19.0, 14.0, 22.0, 18.0, 0, 36.0, 6, 0, 40.0, 12.0, 0, 0, 6.0, 24.0, 20.0, 0, 19.0, 0, 18.0, 0, 39.0, 0, 29.0, 9.0, 0, 0, 0, 0, 0, 9.0, 0, 0, 0, 20.0, 44.0, 29.0, 28.0, 0, 20.0, 0, 2.0, 0, 0],
     "y": ["FECD3", "CJD", "SCA36", "FAME6", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "SCA37", "ADTKD", "FAME7", "SCA6", "OPML1", "SCA4", "OPDM2", "HDL2", "FAME1", "XDP", "SCA10", "OPDM", "FAME3", "NIID", "OPDM4", "FAME4", "SBMA", "SCA31", "SCA12", "OPDM1", "FAME8", "SCA1", "EPM1", "FAME2", "SCA", "SCA3, MJD", "EDM1, PSACH", "SCA17", "SCA2", "FRDA", "GDPAG", "FRA7A", "FRAXE", "FRA2A", "HD", "NME", "EIEE1", "PRTS", "DRPLA", "SCA7", "SCA8", "DM2", "FRA12A", "DM1", "FXS, FXTAS, POF1", "CCHS", "XLMR", "HMNR7"],
     "type": "bar"
   },