32048e16a50722894cf28d9b7b4b050302e38c75 markd Wed Sep 30 17:54:58 2026 -0700 Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain. diff --git src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py index 076b59ca378..aa679e2c153 100755 --- src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py +++ src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py @@ -1,141 +1,141 @@ #!/usr/bin/env python3 """Write the trackDb stanzas for the hg38 hprcPclai composite track. -One subtrack per HPRC Release 2 haplotype, read from the pcLAI GRCh38-coordinate +One subtrack per HPRC Release 2 haplotype, read from the PCLAI GRCh38-coordinate index CSV, so the track follows whatever the index lists rather than a hardcoded sample list. Subtracks are grouped by sample and haplotype so hgTrackUi draws a sample-by-haplotype matrix instead of a flat list of several hundred checkboxes. detailsScript and metaDataUrl are repeated on every subtrack rather than set once on the composite. Both are read as local settings at the point they are used: bigBedClick.c collects detailsScript.* with trackDbLocalSettingsWildMatch(), and hgTrackUi's file fetch looks the path up on the tdb of the clicked track, so a value on the parent alone would not be seen. hprcPclaiMakeTrackDb.py <index.csv> <defaultOnFile> <out.ra> defaultOnFile holds one "<sample>.<haplotype>" per line, the subtracks that start out checked; blank lines and # comments are ignored. """ import sys import csv TRACK = "hprcPclai" GBDB = "/gbdb/$D/hprcPclai" -DATA_VERSION = "HPRC Release 2, pcLAI v1.1 (GRCh38 coordinates)" +DATA_VERSION = "HPRC Release 2, PCLAI v1.1 (GRCh38 coordinates)" # Only four coordinates ever appear in the centroid field across all haplotypes: -# the four ancestry clusters pcLAI discretizes to. They would make a good +# the four ancestry clusters PCLAI discretizes to. They would make a good # categorical filter, but each value contains a comma and comma is the separator # filterValues uses, so filtering on them needs a comma-free label field first. DETAILS_SCRIPT = ('{"dataUrl":"pclaiRefPanel.json","exportFields":["pca","centroid"],' '"title":"Position in ancestry space","xLabel":"PC1","yLabel":"PC2"}') def readIndex(fname): """Return [(sample, haplotype)] from the HPRC index CSV, sorted by sample.""" rows = [] with open(fname, encoding="utf-8", newline="") as fh: for row in csv.DictReader(fh): samp = (row["sample_id"] or "").strip() hap = (row["haplotype"] or "").strip() if samp and hap: rows.append((samp, hap)) if not rows: sys.exit("no rows in %s" % fname) return sorted(set(rows)) def readDefaultOn(fname): on = set() with open(fname, encoding="utf-8") as fh: for line in fh: line = line.split("#")[0].strip() if line: on.add(line) return on def main(): if len(sys.argv) != 4: sys.exit(__doc__) idxFname, onFname, outFname = sys.argv[1:4] haps = readIndex(idxFname) wanted = readDefaultOn(onFname) samples = sorted({s for s, _h in haps}) hapVals = sorted({h for _s, h in haps}) out = open(outFname, "w", encoding="utf-8") w = out.write - w("# hg38 pcLAI local ancestry, one subtrack per HPRC Release 2 haplotype.\n") + w("# hg38 PCLAI local ancestry, one subtrack per HPRC Release 2 haplotype.\n") w("# Generated by hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py -- do not\n") w("# hand-edit; see hg/makeDb/doc/hg38/hprcPclai.txt.\n\n") w("track %s\n" % TRACK) w("compositeTrack on\n") - w("shortLabel pcLAI Ancestry\n") - w("longLabel Point cloud local ancestry inference (pcLAI) along HPRC assembly haplotypes\n") + w("shortLabel PCLAI Ancestry\n") + w("longLabel Point cloud local ancestry inference (PCLAI) along HPRC assembly haplotypes\n") w("group hprc\n") w("type bigBed 9 +\n") w("itemRgb on\n") # dense, and pinned there. This track was on squish only because dense drew # one merged row per subtrack with no per-item map boxes, which left the # mouseOver below and the details-page scatterplot unreachable. denseClick # (#38364) gives a dense row one hgc link and one mouseOver per item, so # dense now does everything squish did and always takes exactly one row per # haplotype, where squish spreads to three or four at whole-chromosome zoom. # denseClick is inherited, so the one line covers all 463 subtracks. # onlyVisibility stays, moved to dense: it is what keeps a reader out of # pack, which at 463 subtracks would be enormous. w("denseClick on\n") w("visibility dense\n") w("onlyVisibility dense\n") w("priority 30\n") # A whole chromosome holds a few thousand windows per haplotype, well over the # 1000-item default at which pack mode gives up drawing; the block structure # this track exists to show is only visible at that zoom. w("maxItems 40000\n") w("subGroup1 sample Sample %s\n" % " ".join("%s=%s" % (s, s) for s in samples)) w("subGroup2 hap Haplotype %s\n" % " ".join("h%s=%s" % (h, h) for h in hapVals)) w("sortOrder sample=+ hap=+\n") w("dimensions dimensionY=sample dimensionX=hap\n") w("dragAndDrop subTracks\n") w("dataVersion %s\n" % DATA_VERSION) w("\n") # Explicit priorities: without them the subtracks come out in an arbitrary # (in practice reversed) order in the image, and with several hundred rows a # stable sample order is what makes the display readable. nOn = 0 for prio, (samp, hap) in enumerate(haps, start=1): key = "%s.%s" % (samp, hap) sub = "%s%sH%s" % (TRACK, samp.replace("-", ""), hap) on = key in wanted nOn += on w(" track %s\n" % sub) w(" parent %s %s\n" % (TRACK, "on" if on else "off")) w(" subGroups sample=%s hap=h%s\n" % (samp, hap)) w(" priority %d\n" % prio) w(" shortLabel %s\n" % key) - w(" longLabel pcLAI ancestry of HPRC assembly %s haplotype %s\n" % (samp, hap)) + w(" longLabel PCLAI ancestry of HPRC assembly %s haplotype %s\n" % (samp, hap)) w(" type bigBed 9 +\n") w(" bigDataUrl %s/%s.bb\n" % (GBDB, key)) w(" itemRgb on\n") w(" mouseOver ${haplotype} ${window}<br>Window PC1,PC2: ${pca}" "<br>Ancestry centroid: ${centroid}<br>Confidence: ${score}\n") w(" detailsScript.scatterPlot.pca %s\n" % DETAILS_SCRIPT) w(" metaDataUrl %s/pclaiRefPanel.json\n" % GBDB) w("\n") out.close() missing = wanted - {"%s.%s" % (s, h) for s, h in haps} if missing: sys.stderr.write("WARNING: default-on not in index: %s\n" % ", ".join(sorted(missing))) sys.stderr.write("%s: %d subtracks, %d samples, %d on by default\n" % (outFname, len(haps), len(samples), nOn)) if __name__ == "__main__": main()