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Fix GWAS fine-mapping postprocessing export #1401

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Merged
gaow merged 1 commit into from
Aug 11, 2026
Merged

Fix GWAS fine-mapping postprocessing export #1401

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14 changes: 9 additions & 5 deletions code/SoS/mnm_analysis/mnm_postprocessing.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -958,7 +958,10 @@
"# `export_suffix` deliberately differs from step 1's `--suffix` (input rds) to avoid CLI collision.\n",
"parameter: export_path = cwd\n",
"parameter: export_prefix = '' # falls back to step-1 `name` if empty\n",
"parameter: export_suffix = 'cis_results_db.rds'\n",
"parameter: export_suffix = '' # empty => derived from `gwas` below\n",
"# Re-declared so the suffix can default by mode: step 1 writes\n",
"# block_results_db.rds under --gwas True, else cis_results_db.rds.\n",
"parameter: gwas = False\n",
"parameter: fsusie_prefix = ''\n",
"parameter: preset_top_loci = False\n",
"# PIP cutoff for getTopLoci; optional independent CS purity (min.abs.corr) cutoff (<0 => none).\n",
Expand All @@ -969,8 +972,9 @@
"\n",
"_pfx = export_prefix if export_prefix else name\n",
"import glob as _glob\n",
"_rds_files = sorted(_glob.glob(f\"{export_path}/{_pfx}.{fsusie_prefix}*.{export_suffix}\"))\n",
"stop_if(len(_rds_files) == 0, f\"No RDS files matched: {export_path}/{_pfx}.{fsusie_prefix}*.{export_suffix}\")\n",
"_suffix = export_suffix if export_suffix else ('block_results_db.rds' if gwas else 'cis_results_db.rds')\n",
"_rds_files = sorted(_glob.glob(f\"{export_path}/{_pfx}.{fsusie_prefix}*.{_suffix}\"))\n",
"stop_if(len(_rds_files) == 0, f\"No RDS files matched: {export_path}/{_pfx}.{fsusie_prefix}*.{_suffix}\")\n",
"_purity_arg = f\"--min-purity {min_purity}\" if float(min_purity) >= 0 else \"\"\n",
"\n",
"input: _rds_files, group_by = 1\n",
Expand Down Expand Up @@ -1019,14 +1023,14 @@
" # header from first non-empty file\n",
" for f in ${_input}; do\n",
" if [ \"$(zcat -f \"$f\" 2>/dev/null | wc -l)\" -ge 2 ]; then\n",
" zcat \"$f\" | head -1\n",
" zcat -f \"$f\" | head -1\n",
" break\n",
" fi\n",
" done\n",
" # data rows from every non-empty file\n",
" for f in ${_input}; do\n",
" if [ \"$(zcat -f \"$f\" 2>/dev/null | wc -l)\" -ge 2 ]; then\n",
" zcat \"$f\" | tail -n +2\n",
" zcat -f \"$f\" | tail -n +2\n",
" fi\n",
" done\n",
" } | $GZ > ${_output}\n"
Expand Down
9 changes: 7 additions & 2 deletions code/script/pecotmr_integration/fine_mapping_cis_db_export.R
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Expand Up @@ -111,8 +111,13 @@ cat(sprintf("Wrote cis_results_db (%d FMR input(s) -> %d rows) + meta (region_id
# ---- 4. pip_sum (optional) -------------------------------------------------
if (!is.na(argv$pip_sum_output)) {
rows <- lapply(seq_len(nrow(db)), function(i) {
sel <- list(study = as.character(db$study[i]), context = as.character(db$context[i]),
trait = as.character(db$trait[i]), method = as.character(db$method[i]))
# NULL-safe per-row identity read: a GwasFineMappingResult has no context /
# trait column, so db$context is NULL and as.character(db$context[i]) would be
# character(0) -- length 0 -- which makes the data.frame() below error on any
# region with signal. Substitute a length-1 NA when the column is absent.
.col1 <- function(nm) { v <- db[[nm]]; if (is.null(v)) NA_character_ else as.character(v[i]) }
sel <- list(study = .col1("study"), context = .col1("context"),
trait = .col1("trait"), method = .col1("method"))
pip <- tryCatch(do.call(getPip, c(list(db), sel)), error = function(e) NULL)
if (is.null(pip)) return(NULL)
data.frame(pip_sum = sum(pip[pip > 0], na.rm = TRUE), condition = sel$context,
Expand Down