8c809888b88a970d262577c31ad2d5a874659788
max
  Thu Sep 17 07:55:41 2026 -0700
hg38: episignatures container with the MethaDory CpG probes

#Preview2 week - bugs introduced now will need a build patch to fix
New alpha superTrack for the CpG positions that published DNA methylation
episignatures are built from. Its first subtrack, MethaDory, holds 268,900
sites drawn from 189 episignatures for 105 rare developmental disorders in 74
studies, compiled by Federico Ferraro and Dmitrijs Rots at Erasmus MC and given
to us for open release.

One row per CpG, merging every episignature that reports it, since a site is
shared by 3.1 signatures on average and by up to 41. The per-signature values
line up as a real table on the details page via detailsDynamicTable; the same
values are also kept as plain columns for the Table Browser and for the
disorder, gene, study and direction filters.

Probe IDs were placed from the Illumina manifests already on the browser, EPIC
850k first, then EPIC v2. Of 847,863 probe-by-signature records, 373 were
dropped because the probe is in none of the manifests; 19,996 of 20,000 sampled
sites land on a CG dinucleotide.

Colour is the direction and size of the strongest effect at the site, split at
a delta-beta of 0.10, plus a conflicting class. Quantile bins were avoided on
purpose: the studies used different reporting cut-offs, so the low end of the
distribution reflects what each paper chose to publish rather than biology.

refs #38371

diff --git src/hg/makeDb/scripts/episignatures/makeHtmlTables.py src/hg/makeDb/scripts/episignatures/makeHtmlTables.py
new file mode 100644
index 00000000000..9e861bcd4d8
--- /dev/null
+++ src/hg/makeDb/scripts/episignatures/makeHtmlTables.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+"""
+Turn studySummary.tsv and locusSummary.tsv into the two HTML tables that go on
+the MethaDory description page. Writes the table markup only; it is pasted into
+methaDory.html between the marker comments.
+"""
+
+import csv
+import html
+import sys
+
+
+def pubLinks(pmidField):
+    out = []
+    for pmid in pmidField.split(","):
+        pmid = pmid.strip()
+        if not pmid:
+            continue
+        if pmid.isdigit():
+            out.append('<a href="https://pubmed.ncbi.nlm.nih.gov/%s/" target="_blank">%s</a>'
+                       % (pmid, pmid))
+        else:
+            out.append('<a href="%s" target="_blank">link</a>' % html.escape(pmid))
+    return ", ".join(out) if out else "&nbsp;"
+
+
+def studyTable(fname, out):
+    out.write('<table class="stdTbl">\n')
+    out.write("<tr><th>Study</th><th>PubMed</th><th>Episignatures</th>"
+              "<th>Disorders</th><th>Probes reported</th><th>Distinct probes</th></tr>\n")
+    with open(fname) as fh:
+        for r in csv.DictReader(fh, delimiter="\t"):
+            out.write("<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td>"
+                      "<td>%s</td><td>%s</td></tr>\n"
+                      % (html.escape(r["study"]), pubLinks(r["pmid"]),
+                         r["signatures"], html.escape(r["disorders"]) or "&nbsp;",
+                         "{:,}".format(int(r["probeRows"])),
+                         "{:,}".format(int(r["uniqProbes"]))))
+    out.write("</table>\n")
+
+
+def locusTable(fname, out):
+    out.write('<table class="stdTbl">\n')
+    out.write("<tr><th>Gene or locus</th><th>Disorders</th><th>Episignatures</th>"
+              "<th>Studies</th><th>Probes reported</th><th>Distinct probes</th></tr>\n")
+    with open(fname) as fh:
+        for r in csv.DictReader(fh, delimiter="\t"):
+            out.write("<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td>"
+                      "<td>%s</td><td>%s</td></tr>\n"
+                      % (html.escape(r["locus"]),
+                         html.escape(r["disorders"]) or "&nbsp;",
+                         r["signatures"], html.escape(r["studies"]),
+                         "{:,}".format(int(r["probeRows"])),
+                         "{:,}".format(int(r["uniqProbes"]))))
+    out.write("</table>\n")
+
+
+which, fname = sys.argv[1], sys.argv[2]
+if which == "studies":
+    studyTable(fname, sys.stdout)
+else:
+    locusTable(fname, sys.stdout)