ed3cb243b9151cae7d1859712148fa1d1e1a2196 lrnassar Mon Apr 13 17:34:17 2026 -0700 Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582 diff --git src/hg/makeDb/scripts/insight/insightPVS1.py src/hg/makeDb/scripts/insight/insightPVS1.py new file mode 100644 index 00000000000..c8f94fe5f47 --- /dev/null +++ src/hg/makeDb/scripts/insight/insightPVS1.py @@ -0,0 +1,348 @@ +#!/usr/bin/env python3 +""" +InSiGHT VCEP PVS1 Decision Track Generator + +This script generates UCSC Genome Browser tracks (bigBed format) for the +InSiGHT Variant Curation Expert Panel (VCEP) PVS1 decision regions +for Lynch syndrome genes: MLH1, MSH2, MSH6, and PMS2. + +The track shows regions where truncating variants receive different ACMG +classifications (PVS1, PVS1_Moderate, or PVS1_n.a.) based on their position. + +Coordinates are computed dynamically from codon positions by querying +NCBI RefSeq transcript coordinates from hgsql for both hg38 and hg19. + +Transcripts used: + MLH1: NM_000249.4 (chr3, + strand) + MSH2: NM_000251.3 (chr2, + strand) + MSH6: NM_000179.3 (chr2, + strand) + PMS2: NM_000535.7 (chr7, - strand) + +Author: Generated for InSiGHT VCEP +Date: 2025 +""" + +import subprocess +import os + +def bash(cmd): + """Run the cmd in bash subprocess""" + try: + rawBashOutput = subprocess.run(cmd, check=True, shell=True, + stdout=subprocess.PIPE, universal_newlines=True, stderr=subprocess.STDOUT) + bashStdoutt = rawBashOutput.stdout + except subprocess.CalledProcessError as e: + raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) + return(bashStdoutt) + +# ============================================================================ +# Configuration +# ============================================================================ +OUTPUT_DIR = "/hive/users/lrnassar/insightHub/pvs1" + +# Transcripts to query +TRANSCRIPTS = { + 'MLH1': 'NM_000249.4', + 'MSH2': 'NM_000251.3', + 'MSH6': 'NM_000179.3', + 'PMS2': 'NM_000535.7', +} + +# PVS1 regions defined by codon ranges +# Format: (gene, name, aa_start, aa_end, color, rule, acmg_code) +# aa_start/aa_end are 1-based codon positions (inclusive) +# Use None for aa_end to indicate "to end of protein" +PVS1_REGIONS = [ + # MLH1 + ('MLH1', 'NMD', 1, 684, '180,0,0', '≤ codon 684', 'PVS1'), + ('MLH1', 'CritRegion', 685, 753, '180,0,0', '> codon 684 ≤ codon 753', 'PVS1'), + ('MLH1', 'FuncUnknown', 754, 756, '204,102,0', 'Codons 754, 755, 756', 'PVS1_Moderate'), + ('MLH1', 'PVS1_n.a.', 757, None, '128,128,128', '> codon 756', 'PVS1_n.a.'), + + # MSH2 + ('MSH2', 'NMD', 1, 861, '180,0,0', '≤ codon 861', 'PVS1'), + ('MSH2', 'CritRegion', 862, 891, '180,0,0', '> codon 861 ≤ codon 891', 'PVS1'), + ('MSH2', 'FuncUnknown', 892, 934, '204,102,0', '> codon 891 ≤ codon 934', 'PVS1_Moderate'), + ('MSH2', 'PVS1_n.a.', 935, None, '128,128,128', '> codon 934', 'PVS1_n.a.'), + + # MSH6 + ('MSH6', 'NMD', 1, 1317, '180,0,0', '≤ codon 1317', 'PVS1'), + ('MSH6', 'CritRegion', 1318, 1341, '180,0,0', '> codon 1317 ≤ codon 1341', 'PVS1'), + ('MSH6', 'FuncUnknown', 1342, 1360, '204,102,0', '> codon 1341 ≤ codon 1360', 'PVS1_Moderate'), + ('MSH6', 'PVS1_n.a.', 1361, None, '128,128,128', '> codon 1360', 'PVS1_n.a.'), + + # PMS2 + ('PMS2', 'NMD', 1, 798, '180,0,0', '≤ codon 798', 'PVS1'), + ('PMS2', 'PVS1_n.a.', 799, None, '128,128,128', '> codon 798', 'PVS1_n.a.'), +] + +# AutoSQL definition for the BED9+3 format +AUTOSQL = """table InSiGHTPVS1 +"InSiGHT VCEP PVS1 decision regions for Lynch syndrome genes (MLH1, MSH2, MSH6, PMS2)" + ( + string chrom; "Reference sequence chromosome or scaffold" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + string name; "Region name (NMD, CritRegion, FuncUnknown, PVS1_n.a.)" + uint score; "Not used, all 0" + char[1] strand; "Not used, all ." + uint thickStart; "Same as chromStart" + uint thickEnd; "Same as chromEnd" + uint reserved; "RGB value (use R,G,B string in input file)" + string rule; "Codon position rule" + string acmgCode; "ACMG classification code" + string _mouseOver; "Field only used as mouseOver" + )""" + +# ============================================================================ +# Functions for coordinate computation +# ============================================================================ + +def get_transcript_info(db, accession): + """Query hgsql to get transcript information from ncbiRefSeq""" + query = f"SELECT name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonEnds FROM ncbiRefSeq WHERE name='{accession}'" + result = bash(f'hgsql {db} -Ne "{query}"') + + if not result.strip(): + raise ValueError(f"Transcript {accession} not found in {db}.ncbiRefSeq") + + fields = result.strip().split('\t') + + # Parse exon starts and ends (comma-separated, trailing comma) + exon_starts = [int(x) for x in fields[7].rstrip(',').split(',')] + exon_ends = [int(x) for x in fields[8].rstrip(',').split(',')] + + return { + 'name': fields[0], + 'chrom': fields[1], + 'strand': fields[2], + 'txStart': int(fields[3]), + 'txEnd': int(fields[4]), + 'cdsStart': int(fields[5]), + 'cdsEnd': int(fields[6]), + 'exonStarts': exon_starts, + 'exonEnds': exon_ends, + } + +def build_cds_regions(tx): + """Build list of CDS regions from transcript info""" + cds_regions = [] + for i in range(len(tx['exonStarts'])): + ex_start = tx['exonStarts'][i] + ex_end = tx['exonEnds'][i] + # Skip exons outside CDS + if ex_end <= tx['cdsStart'] or ex_start >= tx['cdsEnd']: + continue + # Clip exon to CDS boundaries + region_start = max(ex_start, tx['cdsStart']) + region_end = min(ex_end, tx['cdsEnd']) + cds_regions.append((region_start, region_end, i+1)) + + # For minus strand, reverse order (CDS starts from high genomic coords) + if tx['strand'] == '-': + cds_regions = cds_regions[::-1] + + return cds_regions + +def get_protein_length(cds_regions): + """Calculate protein length from CDS regions""" + total_cds_bp = sum(end - start for start, end, _ in cds_regions) + return total_cds_bp // 3 + +def aa_to_genomic_plus(aa_start, aa_end, cds_regions): + """Convert AA range to genomic segments for + strand genes""" + nt_start = (aa_start - 1) * 3 + 1 # 1-based nucleotide position + nt_end = aa_end * 3 + + segments = [] + cumulative = 0 + + for start, end, exon_num in cds_regions: + region_len = end - start + region_nt_start = cumulative + 1 + region_nt_end = cumulative + region_len + + if region_nt_end >= nt_start and region_nt_start <= nt_end: + overlap_nt_start = max(nt_start, region_nt_start) + overlap_nt_end = min(nt_end, region_nt_end) + + genomic_start = start + (overlap_nt_start - region_nt_start) + genomic_end = start + (overlap_nt_end - region_nt_start) + 1 + + segments.append((genomic_start, genomic_end, exon_num)) + + cumulative += region_len + + return segments + +def aa_to_genomic_minus(aa_start, aa_end, cds_regions): + """Convert AA range to genomic segments for - strand genes""" + nt_start = (aa_start - 1) * 3 + 1 + nt_end = aa_end * 3 + + segments = [] + cumulative = 0 + + for start, end, exon_num in cds_regions: + region_len = end - start + region_nt_start = cumulative + 1 + region_nt_end = cumulative + region_len + + if region_nt_end >= nt_start and region_nt_start <= nt_end: + overlap_nt_start = max(nt_start, region_nt_start) + overlap_nt_end = min(nt_end, region_nt_end) + + offset_from_end_start = overlap_nt_start - region_nt_start + offset_from_end_end = overlap_nt_end - region_nt_start + + genomic_end = end - offset_from_end_start + genomic_start = end - offset_from_end_end - 1 + + if genomic_start > genomic_end: + genomic_start, genomic_end = genomic_end, genomic_start + + segments.append((genomic_start, genomic_end, exon_num)) + + cumulative += region_len + + return segments + +def generate_bed_entries(db, transcripts_info): + """Generate BED entries for all PVS1 regions""" + bed_lines = [] + + for gene, name, aa_start, aa_end, color, rule, acmg_code in PVS1_REGIONS: + tx = transcripts_info[gene] + chrom = tx['chrom'] + strand = tx['strand'] + accession = tx['name'] + + cds_regions = build_cds_regions(tx) + protein_length = get_protein_length(cds_regions) + + # If aa_end is None, use protein length + if aa_end is None: + aa_end = protein_length + + # Skip if aa_start is beyond protein length + if aa_start > protein_length: + print(f" WARNING: Skipping {gene} {name} - aa_start ({aa_start}) > protein length ({protein_length})") + continue + + # Clamp aa_end to protein length + if aa_end > protein_length: + aa_end = protein_length + + if strand == '+': + segments = aa_to_genomic_plus(aa_start, aa_end, cds_regions) + else: + segments = aa_to_genomic_minus(aa_start, aa_end, cds_regions) + + for seg_start, seg_end, exon_num in segments: + if seg_start >= seg_end: + print(f" WARNING: Skipping invalid segment for {gene} {name}: {seg_start}-{seg_end}") + continue + + # HTML-encode special characters for mouseOver (UCSC browser can't handle ≤ ≥) + rule_html = rule.replace('≤', '≤').replace('≥', '≥').replace('>', '>').replace('<', '<') + mouse_over = f"<b>Name: </b>{name}</br><b>Gene: </b>{gene}</br><b>Rule: </b>{rule_html}</br><b>ACMG Code: </b>{acmg_code}" + bed_line = f"{chrom}\t{seg_start}\t{seg_end}\t{name}\t0\t.\t{seg_start}\t{seg_end}\t{color}\t{rule}\t{acmg_code}\t{mouse_over}" + bed_lines.append(bed_line) + + return bed_lines + +def create_track(db, output_dir): + """Create BED and bigBed files for a given genome assembly""" + print(f"\n{'='*70}") + print(f"Processing {db}") + print(f"{'='*70}") + + # Query transcript info from hgsql + print(f"\nQuerying transcript coordinates from {db}.ncbiRefSeq...") + transcripts_info = {} + for gene, accession in TRANSCRIPTS.items(): + tx_info = get_transcript_info(db, accession) + cds_regions = build_cds_regions(tx_info) + protein_length = get_protein_length(cds_regions) + print(f" {gene}: {accession} (protein length: {protein_length} aa)") + transcripts_info[gene] = tx_info + + # Generate BED entries + print("\nGenerating BED entries...") + bed_lines = generate_bed_entries(db, transcripts_info) + print(f" Generated {len(bed_lines)} region segments") + + # Write BED file + bed_file = os.path.join(output_dir, f"InSiGHTPVS1_{db}.bed") + print(f"\nWriting BED file: {bed_file}") + with open(bed_file, 'w') as f: + f.write('\n'.join(bed_lines) + '\n') + + # Sort BED file + print("Sorting BED file...") + bash(f"sort -k1,1 -k2,2n {bed_file} -o {bed_file}") + + # Create bigBed + as_file = os.path.join(output_dir, "InSiGHTPVS1.as") + bb_file = os.path.join(output_dir, f"InSiGHTPVS1{db.capitalize()}.bb") + chrom_sizes = f"/cluster/data/{db}/chrom.sizes" + + print(f"\nCreating bigBed file: {bb_file}") + try: + bash(f"bedToBigBed -as={as_file} -type=bed9+3 -tab {bed_file} {chrom_sizes} {bb_file}") + print(f" Successfully created: {bb_file}") + except Exception as e: + print(f" ERROR creating bigBed: {e}") + + return bed_file, bb_file + +# ============================================================================ +# Main execution +# ============================================================================ +if __name__ == "__main__": + print("=" * 70) + print("InSiGHT VCEP PVS1 Decision Track Generator") + print("=" * 70) + + # Create output directory if needed + os.makedirs(OUTPUT_DIR, exist_ok=True) + + # Write AutoSql file + as_file = os.path.join(OUTPUT_DIR, "InSiGHTPVS1.as") + print(f"\nWriting AutoSql file: {as_file}") + with open(as_file, 'w') as f: + f.write(AUTOSQL) + + # Process both assemblies + output_files = {} + for db in ['hg38', 'hg19']: + try: + bed_file, bb_file = create_track(db, OUTPUT_DIR) + output_files[db] = {'bed': bed_file, 'bb': bb_file} + except Exception as e: + print(f"\nERROR processing {db}: {e}") + + # Print summary + print("\n" + "=" * 70) + print("Output Files") + print("=" * 70) + print(f" AutoSql file: {as_file}") + for db, files in output_files.items(): + print(f"\n {db}:") + print(f" BED file: {files['bed']}") + if os.path.exists(files['bb']): + print(f" BigBed file: {files['bb']}") + + print("\n" + "=" * 70) + print("Custom Track Line (for bigBed)") + print("=" * 70) + print(""" + track type=bigBed name="InSiGHT PVS1" \\ + description="InSiGHT VCEP PVS1 Decision Regions" \\ + visibility=pack itemRgb=on \\ + bigDataUrl=<URL_TO_YOUR_BB_FILE> +""") + + print("=" * 70) + print("Done!") + print("=" * 70)