fc7f1b9f5e16f4128f56760ac87a5649ee422b9d angie Thu Mar 26 15:07:25 2020 -0700 Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188 diff --git src/hg/utils/otto/nextstrainNcov/nextstrain.py src/hg/utils/otto/nextstrainNcov/nextstrain.py index e3cd141..373713d 100755 --- src/hg/utils/otto/nextstrainNcov/nextstrain.py +++ src/hg/utils/otto/nextstrainNcov/nextstrain.py @@ -1,244 +1,279 @@ #!/usr/bin/env python3 import json import re from warnings import warn with open('ncov.json') as f: ncov = json.load(f) chrom = 'NC_045512v2' # Genes (to which AA mutations are relative): genePos = {} geneBed = [] for gene,anno in ncov['meta']['genome_annotations'].items(): if (gene != 'nuc'): genePos[gene] = anno['start'] - 1 geneBed.append([chrom, anno['start']-1, anno['end'], gene]) def bedStart(bed): return bed[1] geneBed.sort(key=bedStart) with open('nextstrainGene.bed', 'w') as outG: for bed in geneBed: outG.write('\t'.join(map(str, bed)) + '\n') outG.close() # Variants and "clades" snvRe = re.compile('^([ACGT])([0-9]+)([ACGT])$') snvAaRe = re.compile('^([A-Z*])([0-9]+)([A-Z*])$') clades = {} variantCounts = {} variantAaChanges = {} samples = [] cladeColors = { 'A1a': '73,75,225', 'A2': '75,131,233', 'A2a': '92,173,207', 'A3': '119,199,164', 'A6': '154,212,122', 'A7': '173,189,81', 'B': '233,205,74', 'B1': '255,176,65', 'B2': '255,122,53', 'B4': '249,53,41' } def cladeColorFromName(cladeName): color = cladeColors.get(cladeName); if (not color): color = 'purple' return color def subtractStart(coord, start): return coord - start def cladeFromVariants(name, variants, varStr): """Extract bed12 info from an object whose keys are SNV variant names""" clade = {} snvEnds = [] varNames = [] for varName in variants: m = snvRe.match(varName) if (m): snvEnds.append(int(m.group(2))) varNames.append(varName) if snvEnds: snvEnds.sort() snvStarts = list(map(lambda x: x-1, snvEnds)) snvSizes = list(map(lambda x: 1, snvEnds)) clade['thickStart'] = min(snvStarts) clade['thickEnd'] = max(snvEnds) clade['name'] = name clade['color'] = cladeColorFromName(name) clade['varSizes'] = snvSizes clade['varStarts'] = snvStarts clade['varNames'] = varStr return clade -def numDateToMonthDay(numDate): - """Transform decimal year timestamp to string with only month and day""" +def addDatesToClade(clade, numDateAttrs): + """Add the numeric dates from ncov.json node_attrs.num_date to clade record""" + clade['dateInferred'] = numDateAttrs['value'] + clade['dateConfMin'] = numDateAttrs['confidence'][0] + clade['dateConfMax'] = numDateAttrs['confidence'][1] + +def addDivisionToClade(clade, divisionAttrs): + """Add the administrative division (location) data from ncov.json node_attrs.division to clade""" + clade['divInferred'] = divisionAttrs['value'] + confString = '' + for div, conf in divisionAttrs['confidence'].items(): + if (len(confString)): + confString += ', ' + confString += "%s: %0.5f" % (div, conf) + clade['divConf'] = confString + +def numDateToYmd(numDate): + """Convert numeric date (decimal year) to integer year, month, day""" year = int(numDate) isLeapYear = 1 if (year % 4 == 0) else 0 # Get rid of the year numDate -= year # Convert to Julian day jDay = int(numDate * 365) + 1 if (jDay > 334 + isLeapYear): - monthDay ="Dec" + str(jDay - 334 - isLeapYear) + month, day = 11, (jDay - 334 - isLeapYear) elif (jDay > 304 + isLeapYear): - monthDay ="Nov" + str(jDay - 304 - isLeapYear) + month, day = 10, (jDay - 304 - isLeapYear) elif (jDay > 273 + isLeapYear): - monthDay ="Oct" + str(jDay - 273 - isLeapYear) + month, day = 9, (jDay - 273 - isLeapYear) elif (jDay > 243 + isLeapYear): - monthDay ="Sep" + str(jDay - 243 - isLeapYear) + month, day = 8, (jDay - 243 - isLeapYear) elif (jDay > 212 + isLeapYear): - monthDay ="Aug" + str(jDay - 212 - isLeapYear) + month, day = 7, (jDay - 212 - isLeapYear) elif (jDay > 181 + isLeapYear): - monthDay ="Jul" + str(jDay - 181 - isLeapYear) + month, day = 6, (jDay - 181 - isLeapYear) elif (jDay > 151 + isLeapYear): - monthDay ="Jun" + str(jDay - 151 - isLeapYear) + month, day = 5, (jDay - 151 - isLeapYear) elif (jDay > 120 + isLeapYear): - monthDay ="May" + str(jDay - 120 - isLeapYear) + month, day = 4, (jDay - 120 - isLeapYear) elif (jDay > 90 + isLeapYear): - monthDay ="Apr" + str(jDay - 90 - isLeapYear) + month, day = 3, (jDay - 90 - isLeapYear) elif (jDay > 59 + isLeapYear): - monthDay ="Mar" + str(jDay - 59 - isLeapYear) + month, day = 2, (jDay - 59 - isLeapYear) elif (jDay > 31): - monthDay ="Feb" + str(jDay - 31) + month, day = 1, (jDay - 31) else: - monthDay ="Jan" + str(jDay) - return monthDay + month, day = 0, jDay + return year, month, day + +months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']; + +def numDateToMonthDay(numDate): + """Transform decimal year timestamp to string with only month and day""" + year, month, day = numDateToYmd(numDate) + return months[month] + str(day) + +def numDateToYmdStr(numDate): + """Convert decimal year to YY-MM-DD string""" + year, month, day = numDateToYmd(numDate) + return "%02d-%02d-%02d" % (year, month+1, day) def rUnpackNextstrainTree(branch, parentVariants, parentVarStr): """Recursively descend ncov.tree and build data structures for genome browser tracks""" # Gather variants specific to this node/branch (if any) localVariants = [] if (branch.get('branch_attrs') and branch['branch_attrs'].get('mutations') and branch['branch_attrs']['mutations'].get('nuc')): # Nucleotide variants specific to this branch for varName in branch['branch_attrs']['mutations']['nuc']: if (snvRe.match(varName)): localVariants.append(varName) if (not variantCounts.get(varName)): variantCounts[varName] = 0; # Amino acid variants: figure out which nucleotide variant goes with each for geneName in branch['branch_attrs']['mutations'].keys(): if (geneName != 'nuc'): for change in branch['branch_attrs']['mutations'][geneName]: # Get nucleotide coords & figure out which nuc var this aa change corresponds to aaM = snvAaRe.match(change) if (aaM): aaRef, aaPos, aaAlt = aaM.groups() varStartMin = (int(aaPos) - 1) * 3 if (genePos.get(geneName)): cdsStart = genePos.get(geneName) varStartMin += cdsStart varStartMax = varStartMin + 2 for varName in localVariants: ref, pos, alt = snvRe.match(varName).groups() pos = int(pos) - 1 if (pos >= varStartMin and pos <= varStartMax): variantAaChanges[varName] = geneName + ':' + change else: warn("Can't find start for gene " + geneName) else: warn("Can't match amino acid change" + change) # Inherit parent variants branchVariants = parentVariants.copy() # Add variants specific to this branch (if any) for varName in localVariants: branchVariants[varName] = 1 # Make an ordered variant string as David requested: semicolons between nodes, # comma-separated within a node: branchVarStr = '' for varName in localVariants: if (len(branchVarStr)): branchVarStr += ', ' branchVarStr += varName aaVar = variantAaChanges.get(varName) if (aaVar): branchVarStr += ' (' + aaVar + ')' if (len(parentVarStr) and len(branchVarStr)): branchVarStr = parentVarStr + '; ' + branchVarStr - if (branch['node_attrs'].get('clade_membership')): - cladeName = branch['node_attrs']['clade_membership']['value'] + nodeAttrs = branch['node_attrs'] + if (nodeAttrs.get('clade_membership')): + cladeName = nodeAttrs['clade_membership']['value'] if (not cladeName in clades): clades[cladeName] = cladeFromVariants(cladeName, branchVariants, branchVarStr) + addDatesToClade(clades[cladeName], nodeAttrs['num_date']) + addDivisionToClade(clades[cladeName], nodeAttrs['division']) kids = branch.get('children') if (kids): for child in kids: rUnpackNextstrainTree(child, branchVariants, branchVarStr); else: for varName in branchVariants: variantCounts[varName] += 1 - date = numDateToMonthDay(branch['node_attrs']['num_date']['value']) - samples.append({ 'id': branch['node_attrs']['gisaid_epi_isl']['value'], + samples.append({ 'id': nodeAttrs['gisaid_epi_isl']['value'], 'name': branch['name'], - 'clade': branch['node_attrs']['clade_membership']['value'], - 'date': date, + 'clade': nodeAttrs['clade_membership']['value'], + 'date': numDateToMonthDay(nodeAttrs['num_date']['value']), 'variants': branchVariants }) if (cladeName): if (clades[cladeName].get('sampleCount')): clades[cladeName]['sampleCount'] += 1 else: clades[cladeName]['sampleCount'] = 1 if (clades[cladeName].get('samples')): clades[cladeName]['samples'].append(branch['name']) else: clades[cladeName]['samples'] = [ branch['name'] ] rUnpackNextstrainTree(ncov['tree'], {}, '') sampleCount = len(samples) sampleNames = [ ':'.join([sample['id'], sample['name'], sample['date']]) for sample in samples ] # Parse variant names like 'G11083T' into pos and alleles; bundle in VCF column order parsedVars = [] for varName in variantCounts.keys(): m = snvRe.match(varName) if (m): ref, pos, alt = m.groups() parsedVars.append([int(pos), varName, ref, alt]) else: warn("Can't match " + varName) # Sort by position def parsedVarPos(pv): return pv[0] parsedVars.sort(key=parsedVarPos) def boolToStr01(bool): if (bool): return '1' else: return '0' with open('nextstrainSamples.vcf', 'w') as outC: outC.write('##fileformat=VCFv4.3\n') outC.write('##source=nextstrain.org\n') outC.write('\t'.join(['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']) + '\t' + '\t'.join(sampleNames) + '\n') for pv in parsedVars: varName = pv[1] info = 'AC=' + str(variantCounts[varName]) + ';AN=' + str(sampleCount) aaChange = variantAaChanges.get(varName) if (aaChange): info += ';AACHANGE=' + aaChange genotypes = [] for sample in samples: gt = boolToStr01(sample['variants'].get(varName)) genotypes.append(gt + ':' + sample['clade']) outC.write('\t'.join([ chrom, '\t'.join(map(str, pv)), '\t'.join(['.', 'PASS', info, 'GT:CLADE']), '\t'.join(genotypes) ]) + '\n') outC.close() with open('nextstrainClade.bed', 'w') as outC: for name, clade in clades.items(): if (clade.get('thickStart')): outC.write('\t'.join(map(str, [ chrom, 0, 29903, name, 0, '.', clade['thickStart'], clade['thickEnd'], clade['color'], len(clade['varSizes']) + 2, '1,' + ','.join(map(str, clade['varSizes'])) + ',1,', '0,' + ','.join(map(str, clade['varStarts'])) + ',29902,', clade['varNames'], + numDateToYmdStr(clade['dateInferred']), + numDateToYmdStr(clade['dateConfMin']), + numDateToYmdStr(clade['dateConfMax']), + clade['divInferred'], + clade['divConf'], clade['sampleCount'], ', '.join(clade['samples']) ])) + '\n') outC.close()