1af2fddea7e6ede49cc2b334a6c8e78df998c9fa angie Mon Jun 8 16:15:28 2020 -0700 Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag. Make subtracks for both old and new sets of clades. refs #25188 diff --git src/hg/utils/otto/nextstrainNcov/nextstrain.py src/hg/utils/otto/nextstrainNcov/nextstrain.py index 37b0be1..710773c 100755 --- src/hg/utils/otto/nextstrainNcov/nextstrain.py +++ src/hg/utils/otto/nextstrainNcov/nextstrain.py @@ -17,42 +17,50 @@ 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') # Variants and "clades" snvRe = re.compile('^([ACGT])([0-9]+)([ACGT])$') snvAaRe = re.compile('^([A-Z*])([0-9]+)([A-Z*])$') -clades = {} -cladeNodes = {} +newClades = {} +oldClades = {} variantCounts = {} variantAaChanges = {} samples = [] -cladeColors = { 'A1a': '73,75,225', 'A2': '75,131,233', 'A2a': '92,173,207', +# Clades from March 15th, 2020 to early morning of June 2nd, 2020: +oldCladeColors = { '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): +# Clades from late morning of June 2nd, 2020: +newCladeColors = { '19A': '76,135,232', + '19B': '110,194,178', + '20A': '168,214,110', + '20B': '232,206,75', + '20C': '255,146,58' } + +def cladeColorFromName(cladeName, cladeColors): color = cladeColors.get(cladeName); if (not color): color = '0,0,0' return color def cladeFromVariants(name, variants, varStr): """Extract bed12 info from an object whose keys are SNV variant names""" clade = {} snvEnds = [] # Watch out for back-mutations which make invalid BED because then we have multiple "blocks" # at the same position. Instead, make a back-mutation cancel out the mutation because the # mutation is not found at this node. changesByPos = defaultdict(list) ixsToRemove = [] for varName in variants: @@ -70,51 +78,61 @@ else: ix = len(snvEnds) changesByPos[pos] = (ix, ref, alt) snvEnds.append(int(pos)) if ixsToRemove: ixsToRemove.sort(reverse=True) for ix in ixsToRemove: del snvEnds[ix] if snvEnds: snvEnds.sort() snvStarts = [ e-1 for e in snvEnds ] snvSizes = [ 1 for e in 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 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 addCountryToClade(clade, countryAttrs): """Add country data from ncov.json node_attrs.country to clade""" clade['countryInferred'] = countryAttrs['value'] - confString = '' - for country, conf in countryAttrs['confidence'].items(): - if (len(confString)): - confString += ', ' - confString += "%s: %0.5f" % (country, conf) - clade['countryConf'] = confString + conf = countryAttrs.get('confidence') + clade['countryConf'] = ', '.join([ "%s: %0.5f" % (country, conf) + for country, conf in conf.items()]) if conf else '' + +def processClade(branch, tag, branchVariants, branchVarStr, clades): + """If this is the first time we've seen (old or new) clade, add it to clades""" + nodeAttrs = branch['node_attrs'] + if (nodeAttrs.get(tag)): + cladeName = nodeAttrs[tag]['value'] + if (cladeName != 'unassigned' and not cladeName in clades): + clades[cladeName] = cladeFromVariants(cladeName, branchVariants, branchVarStr) + addDatesToClade(clades[cladeName], nodeAttrs['num_date']) + if (nodeAttrs.get('country')): + addCountryToClade(clades[cladeName], nodeAttrs['country']) + elif (nodeAttrs.get('division')): + addCountryToClade(clades[cladeName], nodeAttrs['division']) + clades[cladeName]['topNode'] = branch 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 daysInYear = 366 if isLeapYear else 365 jDay = int(numDate * daysInYear) + 1 if (jDay > 334 + isLeapYear): month, day = 11, (jDay - 334 - isLeapYear) elif (jDay > 304 + isLeapYear): month, day = 10, (jDay - 304 - isLeapYear) elif (jDay > 273 + isLeapYear): @@ -136,32 +154,35 @@ elif (jDay > 31): month, day = 1, (jDay - 31) else: 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""" + if numDate: year, month, day = numDateToYmd(numDate) return "%02d-%02d-%02d" % (year, month+1, day) + else: + return '' 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(): @@ -190,57 +211,52 @@ 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 elif (not len(branchVarStr)): branchVarStr = parentVarStr - nodeAttrs = branch['node_attrs'] - if (nodeAttrs.get('clade_membership')): - cladeName = nodeAttrs['clade_membership']['value'] - if (cladeName != 'unassigned' and not cladeName in clades): - clades[cladeName] = cladeFromVariants(cladeName, branchVariants, branchVarStr) - addDatesToClade(clades[cladeName], nodeAttrs['num_date']) - if (nodeAttrs.get('country')): - addCountryToClade(clades[cladeName], nodeAttrs['country']) - elif (nodeAttrs.get('division')): - addCountryToClade(clades[cladeName], nodeAttrs['division']) - else: - warn('No country or division for new clade ' + cladeName) - cladeNodes[cladeName] = branch + processClade(branch, 'clade_membership', branchVariants, branchVarStr, newClades) + processClade(branch, 'legacy_clade_membership', branchVariants, branchVarStr, oldClades) kids = branch.get('children') if (kids): for child in kids: rUnpackNextstrainTree(child, branchVariants, branchVarStr); else: for varName in branchVariants: variantCounts[varName] += 1 + nodeAttrs = branch['node_attrs'] if (nodeAttrs.get('submitting_lab')): lab = nodeAttrs['submitting_lab']['value'] else: lab = '' + if (nodeAttrs.get('legacy_clade_membership')): + oldClade = nodeAttrs['legacy_clade_membership']['value'] + else: + oldClade = '' samples.append({ 'id': nodeAttrs['gisaid_epi_isl']['value'], 'name': branch['name'], 'clade': nodeAttrs['clade_membership']['value'], + 'oldClade': oldClade, 'date': numDateToMonthDay(nodeAttrs['num_date']['value']), 'lab': lab, 'variants': branchVariants, 'varStr': branchVarStr }) rUnpackNextstrainTree(ncov['tree'], {}, '') def sampleName(sample): return '|'.join([sample['id'], sample['name'], sample['date']]) sampleCount = len(samples) sampleNames = [ sampleName(sample) for sample in samples ] # Parse variant names like 'G11083T' into pos and alleles; bundle in VCF column order parsedVars = [] @@ -324,76 +340,84 @@ aaChanges = [] for varName in varNames: aaChange = variantAaChanges.get(varName) if (aaChange): gotAaChange = 1 aaChanges.append(aaChange) else: aaChanges.append('-'); if (gotAaChange): aaChangeStr = ','.join(aaChanges) else: aaChangeStr = '' return aaChangeStr # VCF -with open('nextstrainSamples.vcf', 'w') as outC: +def vcfForAll(fileName, cladeTag): + with open(fileName, 'w') as outC: writeVcfHeaderExceptSamples(outC) outC.write('\t'.join(sampleNames) + '\n') for mv in mergedVars: pv, alts, altCounts, sampleAlleles, backMutSamples = mv info = 'AC=' + ','.join(map(str, altCounts)) + ';AN=' + str(sampleCount) varNameMerged = pv[1] aaChange = tallyAaChanges(varNameMerged) if (len(aaChange)): info += ';AACHANGE=' + aaChange if (len(backMutSamples)): info += ';BACKMUTS=' + ','.join(backMutSamples) genotypes = [] for sample, alIx in zip(samples, sampleAlleles): gt = str(alIx) - genotypes.append(gt + ':' + sample['clade']) + genotypes.append(gt + ':' + sample[cladeTag]) outC.write('\t'.join([ chrom, '\t'.join(map(str, pv)), '\t'.join(['.', 'PASS', info, 'GT:CLADE']), '\t'.join(genotypes) ]) + '\n') +vcfForAll('nextstrainSamples.vcf', 'clade') +# I'll skip writing an enormous file with wasteful clades-in-genotypes... really need +# a sample metadata file! + # Assign samples to clades; a sample can appear in multiple clades if they are nested. -cladeSamples = {} -cladeSampleCounts = {} -cladeSampleNames = {} -def sampleIdsFromNode(node, ids): - """Fill in a dict of IDs of all samples found under node.""" +def sampleIdsFromNode(node, cladeTops=()): + """Return a list of IDs of all samples found under node.""" kids = node.get('children') if (kids): + sampleIds = [] for kid in kids: - sampleIdsFromNode(kid, ids) + if (kid not in cladeTops): + sampleIds += sampleIdsFromNode(kid, cladeTops) else: sampleId = node['node_attrs']['gisaid_epi_isl']['value'] - ids[sampleId] = 1 + sampleIds = [sampleId] + return sampleIds -for cladeName, node in cladeNodes.items(): - sampleIds = {} - sampleIdsFromNode(node, sampleIds) - cladeSampleList = [ sample for sample in samples if sample['id'] in sampleIds ] - cladeSamples[cladeName] = sampleIds +cladeSampleCounts = {} +cladeSampleNames = {} + +def vcfForClades(clades, cladeTops=()): + """Given a set of clades (old or new), dump out VCF for each clade. + Stop at nodes in cladeTops (for Nextstrain's new clade scheme where 19A is root, 20A fully + contains 20B and 20C, etc.""" + for cladeName in clades: + node = clades[cladeName]['topNode'] + cladeSampleIds = set(sampleIdsFromNode(node, cladeTops)) + cladeSampleList = [ sample for sample in samples if sample['id'] in cladeSampleIds ] cladeSampleCounts[cladeName] = len(cladeSampleList) cladeSampleNames[cladeName] = [ sampleName(sample) for sample in cladeSampleList ] - -# Per-clade VCF subset -for cladeName, cladeSampleIds in cladeSamples.items(): with open('nextstrainSamples' + cladeName + '.vcf', 'w') as outV: writeVcfHeaderExceptSamples(outV) outV.write('\t'.join(cladeSampleNames[cladeName]) + '\n') for mv in mergedVars: pv, alts, overallAltCounts, sampleAlleles, backMutSamples = mv varNameMerged = pv[1] genotypes = [] altCounts = [ 0 for alt in alts ] acTotal=0 for sample, alIx in zip(samples, sampleAlleles): if (sample['id'] in cladeSampleIds): gt = str(alIx) genotypes.append(gt + ':' + cladeName) if (alIx > 0): altCounts[alIx - 1] += 1 @@ -401,103 +425,144 @@ if (acTotal > 0): info = 'AC=' + ','.join(map(str, altCounts)) info += ';AN=' + str(cladeSampleCounts[cladeName]) aaChange = tallyAaChanges(varNameMerged) if (len(aaChange)): info += ';AACHANGE=' + aaChange cladeBackMuts = [ sampleName for sampleName in backMutSamples if sampleName in cladeSampleNames[cladeName] ] if (len(cladeBackMuts)): info += ';BACKMUTS=' + ','.join(cladeBackMuts) outV.write('\t'.join([ chrom, '\t'.join(map(str, pv)), '\t'.join(['.', 'PASS', info, 'GT:CLADE']), '\t'.join(genotypes) ]) + '\n') -# BED+ file for clades -with open('nextstrainClade.bed', 'w') as outC: +def bedForClades(fileName, clades, cladeColors): + """Make a BED file summarizing each clade""" + with open(fileName, 'w') as outC: for name, clade in clades.items(): - if (clade.get('thickStart')): + if (not clade.get('thickStart')): + # "Clade" 19A encompasses the entire tree (minus the parts assigned to + # other "clades"). It has no identifying variants, and (as of June 7) + # no dates assigned. + clade['thickStart'] = clade['thickEnd'] = 0 + clade['varStarts'] = clade['varSizes'] = [] + clade['varNames'] = '' + clade['dateInferred'] = clade['dateConfMin'] = clade['dateConfMax'] = 0 + countryConf = clade.get('countryConf') + if (not countryConf): + countryConf = '' + countryInferred = clade.get('countryInferred') + if (not countryInferred): + countryInferred = '' outC.write('\t'.join(map(str, [ chrom, 0, 29903, name, 0, '.', - clade['thickStart'], clade['thickEnd'], clade['color'], + clade['thickStart'], clade['thickEnd'], + cladeColorFromName(name, cladeColors), len(clade['varSizes']) + 2, - '1,' + ','.join(map(str, clade['varSizes'])) + ',1,', - '0,' + ','.join(map(str, clade['varStarts'])) + ',29902,', + ','.join(map(str, ([1] + clade['varSizes']) + [1])), + ','.join(map(str, ([0] + clade['varStarts']) + [29902])), clade['varNames'], numDateToYmdStr(clade['dateInferred']), numDateToYmdStr(clade['dateConfMin']), numDateToYmdStr(clade['dateConfMax']), - clade['countryInferred'], - clade['countryConf'], + countryInferred, + countryConf, cladeSampleCounts[name], ', '.join(cladeSampleNames[name]) ])) + '\n') +if (len(oldClades) == 0): + # This ncov.json must be from when old clades were the new clades, and the new clades + # had not yet arrived. Revert to old colors and don't exclude subclades. + newCladeColors = oldCladeColors + newCladeTops = () +else: + newCladeTops = [ newClades[cladeName]['topNode'] for cladeName in newClades ] +vcfForClades(newClades, newCladeTops) +bedForClades('nextstrainClade.bed', newClades, newCladeColors) +if (len(oldClades)): + vcfForClades(oldClades) + bedForClades('nextstrainOldClade.bed', oldClades, oldCladeColors) + # Newick-formatted tree of samples for VCF display -def cladeRgbFromName(cladeName): +def cladeRgbFromName(cladeName, cladeColors): """Look up the r,g,b string color for clade; convert to int RGB.""" - rgbCommaStr = cladeColorFromName(cladeName) + rgbCommaStr = cladeColorFromName(cladeName, cladeColors) r, g, b = [ int(x) for x in rgbCommaStr.split(',') ] rgb = (r << 16) | (g << 8) | b return rgb -def rNextstrainToNewick(node, parentClade=None, parentVarStr=''): - """Recursively descend ncov.tree and build Newick tree string of samples to file""" +def rNextstrainToNewick(node, cladeColors, cladeTops=(), parentClade=None, parentVarStr=''): + """Recursively descend ncov.tree and build Newick tree string of samples to file. + Exclude nodes in cladeTops.""" kids = node.get('children') if (kids): # Make a more concise variant path string than the one we make for the clade track, # to embed in internal node labels for Yatish's tree explorations. localVariants = [] if (node.get('branch_attrs') and node['branch_attrs'].get('mutations') and node['branch_attrs']['mutations'].get('nuc')): # Nucleotide variants specific to this branch for varName in node['branch_attrs']['mutations']['nuc']: if (snvRe.match(varName)): localVariants.append(varName) varStr = '+'.join(localVariants) if (len(parentVarStr) and len(varStr)): varStr = '$'.join([parentVarStr, varStr]) elif (not len(varStr)): varStr = parentVarStr nodeAttrs = node['node_attrs'] if (nodeAttrs.get('clade_membership')): cladeName = nodeAttrs['clade_membership']['value'] elif (parentClade): cladeName = parentClade else: cladeName = 'unassigned' - color = str(cladeRgbFromName(cladeName)) - descendants = ','.join([ rNextstrainToNewick(child, cladeName, varStr) for child in kids ]) + color = str(cladeRgbFromName(cladeName, cladeColors)) + descendants = ','.join([ rNextstrainToNewick(child, cladeColors, cladeTops, cladeName, + varStr) + for child in kids if child not in cladeTops ]) label = '#'.join([cladeName, varStr]) treeString = '(' + descendants + ')' + label + ':' + color else: nodeAttrs = node['node_attrs'] gId = nodeAttrs['gisaid_epi_isl']['value'] name = node['name'] date = numDateToMonthDay(nodeAttrs['num_date']['value']) cladeName = nodeAttrs['clade_membership']['value'] - color = str(cladeRgbFromName(cladeName)) + color = str(cladeRgbFromName(cladeName, cladeColors)) treeString = sampleName({ 'id': gId, 'name': name, 'date': date }) + ':' + color return treeString with open('nextstrain.nh', 'w') as outF: - outF.write(rNextstrainToNewick(ncov['tree']) + ';\n') + outF.write(rNextstrainToNewick(ncov['tree'], newCladeColors) + ';\n') -for cladeName, node in cladeNodes.items(): +if (len(oldClades)): + with open('nextstrainOldCladeColors.nh', 'w') as outF: + outF.write(rNextstrainToNewick(ncov['tree'], oldCladeColors) + ';\n') + +def newickForClades(clades, cladeColors, cladeTops=()): + for cladeName in clades: filename = 'nextstrain' + cladeName + '.nh' + node = clades[cladeName]['topNode'] with open(filename, 'w') as outF: - outF.write(rNextstrainToNewick(node) + ';\n') + outF.write(rNextstrainToNewick(node, cladeColors, cladeTops) + ';\n') + +newickForClades(newClades, newCladeColors, newCladeTops) +if (len(oldClades)): + newickForClades(oldClades, oldCladeColors) # File with samples and their clades, labs and variant paths apostropheSRe = re.compile("'s"); firstLetterRe = re.compile('(\w)\w+'); spacePunctRe = re.compile('\W'); def abbreviateLab(lab): """Lab names are very long and sometimes differ by punctuation or typos. Abbreviate for easier comparison.""" labAbbrev = apostropheSRe.sub('', lab) labAbbrev = firstLetterRe.sub(r'\1', labAbbrev, count=0) labAbbrev = spacePunctRe.sub('', labAbbrev, count=0) return labAbbrev with open('nextstrainSamples.varPaths', 'w') as outF: