1ab96609fb58d6c6053425989043e9e7c5dd9f99 angie Mon Jan 10 08:56:42 2022 -0800 Update Nextstrain clade names and color spectrum in Auspice JSON output. diff --git src/hg/hgPhyloPlace/treeToAuspiceJson.c src/hg/hgPhyloPlace/treeToAuspiceJson.c index f704622..02e6bed 100644 --- src/hg/hgPhyloPlace/treeToAuspiceJson.c +++ src/hg/hgPhyloPlace/treeToAuspiceJson.c @@ -1,627 +1,627 @@ /* Convert a (sub)tree with condensed nodes to JSON for Nextstrain to display, adding in sample * mutations, protein changes and metadata. */ /* Copyright (C) 2020 The Regents of the University of California */ #include "common.h" #include "hash.h" #include "hui.h" #include "jsonWrite.h" #include "linefile.h" #include "parsimonyProto.h" #include "phyloPlace.h" #include "phyloTree.h" #include "variantProjector.h" // Globals extern char *chrom; extern int chromSize; static void writeAuspiceMeta(FILE *outF, struct slName *subtreeUserSampleIds, char *source) /* Write metadata to configure Auspice display. */ { fprintf(outF, "\"meta\": { " "\"title\": \"Subtree with %s", subtreeUserSampleIds->name); int sampleCount = slCount(subtreeUserSampleIds); if (sampleCount > 10) fprintf(outF, " and %d other uploaded samples", sampleCount - 1); else { struct slName *sln; for (sln = subtreeUserSampleIds->next; sln != NULL; sln = sln->next) fprintf(outF, ", %s", sln->name); } fputs("\", " "\"panels\": [ \"tree\"] , " "\"colorings\": [ " " { \"key\": \"pango_lineage\", " " \"title\": \"Pango lineage\", \"type\": \"categorical\" }," " { \"key\": \"Nextstrain_clade\"," " \"scale\": [ " - " [ \"20H (Beta, V2)\", \"#3F47C9\" ]," - " [ \"20I (Alpha, V1)\", \"#4274CE\" ]," - " [ \"20J (Gamma, V3)\", \"#4F97BB\" ]," - " [ \"21A (Delta)\", \"#64AC99\" ]," - " [ \"21B (Kappa)\", \"#7EB976\" ]," - " [ \"21C (Epsilon)\", \"#9EBE5A\" ]," - " [ \"21D (Eta)\", \"#BEBB48\" ]," - " [ \"21E (Theta)\", \"#D9AE3E\" ]," - " [ \"21F (Iota)\", \"#E69036\" ]," - " [ \"21G (Lambda)\", \"#E35F2D\" ]," - " [ \"21H\", \"#DB2823\" ]," + " [ \"20H (Beta, V2)\", \"#571EA2\" ]," + " [ \"20I (Alpha, V1)\", \"#4334BF\" ]," + " [ \"20J (Gamma, V3)\", \"#3F55CE\" ]," + " [ \"21A (Delta)\", \"#4376CD\" ]," + " [ \"21I (Delta)\", \"#4C91C0\" ]," + " [ \"21J (Delta)\", \"#59A4A9\" ]," + " [ \"21C (Epsilon)\", \"#7FB975\" ]," + " [ \"21D (Eta)\", \"#97BD5F\" ]," + " [ \"21F (Iota)\", \"#C7B944\" ]," + " [ \"21G (Lambda)\", \"#D9AD3D\" ]," + " [ \"21H (Mu)\", \"#E49838\" ]," + " [ \"21K (Omicron)\", \"#DB2823\" ]," + " [ \"21L (Omicron)\", \"#DB2823\" ]," + " [ \"21M (Omicron)\", \"#DB2823\" ]," " [ \"uploaded sample\", \"#FF0000\" ] ]," " \"title\": \"Nextstrain Clade\", \"type\": \"categorical\" }," , outF); if (sameString(source, "GISAID")) fputs(" { \"key\": \"GISAID_clade\"," " \"scale\": [ [ \"S\", \"#EC676D\" ], [ \"L\", \"#F79E43\" ], [ \"O\", \"#F9D136\" ]," " [ \"V\", \"#FAEA95\" ], [ \"G\", \"#B6D77A\" ], [ \"GH\", \"#8FD4ED\" ]," " [ \"GR\", \"#A692C3\" ] ]," " \"title\": \"GISAID Clade\", \"type\": \"categorical\" }," , outF); fprintf(outF, " { \"key\": \"pango_lineage_usher\", " " \"title\": \"Pango lineage assigned by UShER\", \"type\": \"categorical\" }," " { \"key\": \"Nextstrain_clade_usher\"," " \"scale\": [ " - " [ \"20H(Beta, V2)\", \"#3F47C9\" ]," - " [ \"20I(Alpha, V1)\", \"#4274CE\" ]," - " [ \"20J(Gamma, V3)\", \"#4F97BB\" ]," - " [ \"21A(Delta)\", \"#64AC99\" ]," - " [ \"21B(Kappa)\", \"#7EB976\" ]," - " [ \"21C(Epsilon)\", \"#9EBE5A\" ]," - " [ \"21D(Eta)\", \"#BEBB48\" ]," - " [ \"21E(Theta)\", \"#D9AE3E\" ]," - " [ \"21F(Iota)\", \"#E69036\" ]," - " [ \"21G(Lambda)\", \"#E35F2D\" ]," - " [ \"20H (Beta, V2)\", \"#3F47C9\" ]," - " [ \"20I (Alpha, V1)\", \"#4274CE\" ]," - " [ \"20J (Gamma, V3)\", \"#4F97BB\" ]," - " [ \"21A (Delta)\", \"#64AC99\" ]," - " [ \"21B (Kappa)\", \"#7EB976\" ]," - " [ \"21C (Epsilon)\", \"#9EBE5A\" ]," - " [ \"21D (Eta)\", \"#BEBB48\" ]," - " [ \"21E (Theta)\", \"#D9AE3E\" ]," - " [ \"21F (Iota)\", \"#E69036\" ]," - " [ \"21G (Lambda)\", \"#E35F2D\" ]," - " [ \"21H\", \"#DB2823\" ]," + " [ \"20H (Beta, V2)\", \"#571EA2\" ]," + " [ \"20I (Alpha, V1)\", \"#4334BF\" ]," + " [ \"20J (Gamma, V3)\", \"#3F55CE\" ]," + " [ \"20H (Beta,V2)\", \"#571EA2\" ]," + " [ \"20I (Alpha,V1)\", \"#4334BF\" ]," + " [ \"20J (Gamma,V3)\", \"#3F55CE\" ]," + " [ \"21A (Delta)\", \"#4376CD\" ]," + " [ \"21I (Delta)\", \"#4C91C0\" ]," + " [ \"21J (Delta)\", \"#59A4A9\" ]," + " [ \"21C (Epsilon)\", \"#7FB975\" ]," + " [ \"21D (Eta)\", \"#97BD5F\" ]," + " [ \"21F (Iota)\", \"#C7B944\" ]," + " [ \"21G (Lambda)\", \"#D9AD3D\" ]," + " [ \"21H (Mu)\", \"#E49838\" ]," + " [ \"21K (Omicron)\", \"#DB2823\" ]," + " [ \"21L\", \"#DB2823\" ]," + " [ \"21L (Omicron)\", \"#DB2823\" ]," + " [ \"21M (Omicron)\", \"#DB2823\" ]," " [ \"uploaded sample\", \"#FF0000\" ] ]," " \"title\": \"Nextstrain Clade assigned by UShER\", \"type\": \"categorical\" }," " { \"key\": \"userOrOld\", " " \"scale\": [ [ \"uploaded sample\", \"#CC0000\"] , [ \"%s\", \"#000000\"] ]," " \"title\": \"Sample type\", \"type\": \"categorical\" }," " {\"key\": \"gt\", \"title\": \"Genotype\", \"type\": \"categorical\"}," " {\"key\": \"country\", \"title\": \"Country\", \"type\": \"categorical\"}" , source); fputs(" ] , " //#*** Filters didn't seem to work... maybe something about the new fetch feature, or do I need to spcify in some other way? //#*** "\"filters\": [ \"GISAID_clade\", \"region\", \"country\", \"division\", \"author\" ], " "\"filters\": [ ], " "\"genome_annotations\":" "{\"E\":{\"end\":26472,\"start\":26245,\"strand\":\"+\",\"type\":\"CDS\"}," " \"M\":{\"end\":27191,\"start\":26523,\"strand\":\"+\",\"type\":\"CDS\"}," " \"N\":{\"end\":29533,\"start\":28274,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF1ab\":{\"end\":21555,\"start\":266,\"strand\":\"+\",\"type\":\"CDS\"}," // " \"ORF1a\":{\"end\":13468,\"start\":266,\"strand\":\"+\",\"type\":\"CDS\"}," // " \"ORF1b\":{\"end\":21555,\"start\":13468,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF3a\":{\"end\":26220,\"start\":25393,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF6\":{\"end\":27387,\"start\":27202,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF7a\":{\"end\":27759,\"start\":27394,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF7b\":{\"end\":27887,\"start\":27756,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF8\":{\"end\":28259,\"start\":27894,\"strand\":\"+\",\"type\":\"CDS\"}," " \"ORF9b\":{\"end\":28577,\"start\":28284,\"strand\":\"+\",\"type\":\"CDS\"}," " \"S\":{\"end\":25384,\"start\":21563,\"strand\":\"+\",\"type\":\"CDS\"}," " \"nuc\":{\"end\":29903,\"start\":1,\"strand\":\"+\",\"type\":\"source\"}}," "\"display_defaults\": { " " \"branch_label\": \"none\", " " \"color_by\": \"Nextstrain_clade\" " "}, " , outF); fprintf(outF, "\"description\": \"Dataset generated by [UShER web interface]" "(%shgPhyloPlace) using the " "[usher](https://github.com/yatisht/usher/) program. " //#*** TODO: describe input from which tree was generated: user sample, version of tree, etc. , hLocalHostCgiBinUrl()); fputs("If you have metadata you wish to display, you can now drag on a CSV file and it will be " "added into this view, [see here]("NEXTSTRAIN_DRAG_DROP_DOC") " "for more info.\"} ," , outF); } static void jsonWriteObjectValueUrl(struct jsonWrite *jw, char *name, char *value, char *url) /* Write an object with member "value" set to value, and if url is non-empty, "url" set to url. */ { jsonWriteObjectStart(jw, name); jsonWriteString(jw, "value", value); if (isNotEmpty(url)) jsonWriteString(jw, "url", url); jsonWriteObjectEnd(jw); } static void jsonWriteObjectValue(struct jsonWrite *jw, char *name, char *value) /* Write an object with one member, "value", set to value, as most Auspice node attributes are * formatted. */ { jsonWriteObjectValueUrl(jw, name, value, NULL); } static void makeLineageUrl(char *lineage, char *lineageUrl, size_t lineageUrlSize) /* If lineage is not "uploaded sample", make an outbreak.info link to it, otherwise just copy * lineage. */ { if (sameString(lineage, "uploaded sample")) safecpy(lineageUrl, lineageUrlSize, lineage); else safef(lineageUrl, lineageUrlSize, OUTBREAK_INFO_URLBASE "%s", lineage); } static void jsonWriteLeafNodeAttributes(struct jsonWrite *jw, char *name, struct sampleMetadata *met, boolean isUserSample, char *source, struct hash *sampleUrls, char **retUserOrOld, char **retNClade, char **retGClade, char **retLineage, char **retNCladeUsher, char **retLineageUsher) /* Write elements of node_attrs for a sample which may be preexisting and in our metadata hash, * or may be a new sample from the user. Set rets for color categories so parent branches can * determine their color categories. */ { *retUserOrOld = isUserSample ? "uploaded sample" : source; jsonWriteObjectValue(jw, "userOrOld", *retUserOrOld); if (met && met->date) jsonWriteObjectValue(jw, "date", met->date); if (met && met->author) { jsonWriteObjectValue(jw, "author", met->author); // Note: Nextstrain adds paper_url and title when available; they also add author and use // a uniquified value (e.g. "author": "Wenjie Tan et al" / "value": "Wenjie Tan et al A") } *retNClade = isUserSample ? "uploaded sample" : (met && met->nClade) ? met->nClade : NULL; if (isNotEmpty(*retNClade)) jsonWriteObjectValue(jw, "Nextstrain_clade", *retNClade); *retGClade = isUserSample ? "uploaded sample" : (met && met->gClade) ? met->gClade : NULL; if (isNotEmpty(*retGClade)) jsonWriteObjectValue(jw, "GISAID_clade", *retGClade); *retLineage = isUserSample ? "uploaded sample" : (met && met->lineage) ? met->lineage : NULL; if (isNotEmpty(*retLineage)) { char lineageUrl[1024]; makeLineageUrl(*retLineage, lineageUrl, sizeof lineageUrl); jsonWriteObjectValueUrl(jw, "pango_lineage", *retLineage, lineageUrl); } if (met && met->epiId) jsonWriteObjectValue(jw, "gisaid_epi_isl", met->epiId); if (met && met->gbAcc) jsonWriteObjectValue(jw, "genbank_accession", met->gbAcc); if (met && met->country) jsonWriteObjectValue(jw, "country", met->country); if (met && met->division) jsonWriteObjectValue(jw, "division", met->division); if (met && met->location) jsonWriteObjectValue(jw, "location", met->location); if (met && met->countryExp) jsonWriteObjectValue(jw, "country_exposure", met->countryExp); if (met && met->divExp) jsonWriteObjectValue(jw, "division_exposure", met->divExp); if (met && met->origLab) jsonWriteObjectValue(jw, "originating_lab", met->origLab); if (met && met->subLab) jsonWriteObjectValue(jw, "submitting_lab", met->subLab); if (met && met->region) jsonWriteObjectValue(jw, "region", met->region); *retNCladeUsher = isUserSample ? "uploaded sample" : (met && met->nCladeUsher) ? met->nCladeUsher : NULL; if (isNotEmpty(*retNCladeUsher)) jsonWriteObjectValue(jw, "Nextstrain_clade_usher", *retNCladeUsher); *retLineageUsher = isUserSample ? "uploaded sample" : (met && met->lineageUsher) ? met->lineageUsher : NULL; if (isNotEmpty(*retLineageUsher)) { char lineageUrl[1024]; makeLineageUrl(*retLineageUsher, lineageUrl, sizeof lineageUrl); jsonWriteObjectValueUrl(jw, "pango_lineage_usher", *retLineageUsher, lineageUrl); } char *sampleUrl = (sampleUrls && name) ? hashFindVal(sampleUrls, name) : NULL; if (isNotEmpty(sampleUrl)) { char *p = strstr(sampleUrl, "subtreeAuspice"); char *subtreeNum = p + strlen("subtreeAuspice"); if (p && isdigit(*subtreeNum)) { int num = atoi(subtreeNum); char subtreeLabel[1024]; safef(subtreeLabel, sizeof subtreeLabel, "view subtree %d", num); jsonWriteObjectValueUrl(jw, "subtree", subtreeLabel, sampleUrl); } else jsonWriteObjectValueUrl(jw, "subtree", sampleUrl, sampleUrl); } } static void jsonWriteBranchNodeAttributes(struct jsonWrite *jw, char *userOrOld, char *nClade, char *gClade, char *lineage, char *nCladeUsher, char *lineageUsher) /* Write elements of node_attrs for a branch. */ { if (userOrOld) jsonWriteObjectValue(jw, "userOrOld", userOrOld); if (nClade) jsonWriteObjectValue(jw, "Nextstrain_clade", nClade); if (gClade) jsonWriteObjectValue(jw, "GISAID_clade", gClade); if (lineage) jsonWriteObjectValue(jw, "pango_lineage", lineage); if (nCladeUsher) jsonWriteObjectValue(jw, "Nextstrain_clade_usher", nCladeUsher); if (lineageUsher) jsonWriteObjectValue(jw, "pango_lineage_usher", lineageUsher); } static boolean changesProtein(struct singleNucChange *snc, struct geneInfo *gi, struct seqWindow *gSeqWin, int *retAaStart, char *retOldAa, char *retNewAa) /* If snc changes the coding sequence of gene, return TRUE and set ret values accordingly * (note amino acid values are single-base not strings). */ { boolean isCodingChange = FALSE; if (snc->chromStart < gi->psl->tEnd && snc->chromStart >= gi->psl->tStart) { struct bed3 gBed3 = { NULL, chrom, snc->chromStart, snc->chromStart+1 }; char gAlt[2]; safef(gAlt, sizeof(gAlt), "%c", snc->newBase); if (!sameString(gi->psl->strand, "+")) errAbort("changesProtein: only works for psl->strand='+', but gene '%s' has strand '%s'", gi->psl->qName, gi->psl->strand); struct vpTx *vpTx = vpGenomicToTranscript(gSeqWin, &gBed3, gAlt, gi->psl, gi->txSeq); if (vpTx->start.region == vpExon) { int aaStart = vpTx->start.txOffset / 3; int codonStart = aaStart * 3; char newCodon[4]; safencpy(newCodon, sizeof newCodon, gi->txSeq->dna + codonStart, 3); int codonOffset = vpTx->start.txOffset - codonStart; assert(codonOffset < sizeof newCodon); newCodon[codonOffset] = snc->newBase; char newAa = lookupCodon(newCodon); char oldAa; if (snc->parBase == snc->refBase) oldAa = lookupCodon(gi->txSeq->dna + codonStart); else { char oldCodon[4]; safencpy(oldCodon, sizeof oldCodon, gi->txSeq->dna + codonStart, 3); oldCodon[codonOffset] = snc->parBase; oldAa = lookupCodon(oldCodon); } // Watch out for lookupCodon's null-character return value for stop codon; we want '*'. if (newAa == '\0') newAa = '*'; if (oldAa == '\0') oldAa = '*'; if (newAa != oldAa) { isCodingChange = TRUE; *retAaStart = aaStart; *retOldAa = oldAa; *retNewAa = newAa; } } vpTxFree(&vpTx); } return isCodingChange; } struct slPair *getAaMutations(struct singleNucChange *sncList, struct geneInfo *geneInfoList, struct seqWindow *gSeqWin) /* Given lists of SNVs and genes, return a list of pairs of { gene name, AA change list }. */ { struct slPair *geneChangeList = NULL; struct geneInfo *gi; for (gi = geneInfoList; gi != NULL; gi = gi->next) { struct slName *aaChangeList = NULL; struct singleNucChange *snc; for (snc = sncList; snc != NULL; snc = snc->next) { if (snc->chromStart < gi->psl->tEnd && snc->chromStart >= gi->psl->tStart) { int aaStart; char oldAa, newAa; if (changesProtein(snc, gi, gSeqWin, &aaStart, &oldAa, &newAa)) { char aaChange[32]; safef(aaChange, sizeof aaChange, "%c%d%c", oldAa, aaStart+1, newAa); slNameAddHead(&aaChangeList, aaChange); } } } if (aaChangeList != NULL) { slReverse(&aaChangeList); slAddHead(&geneChangeList, slPairNew(gi->psl->qName, aaChangeList)); } } slReverse(&geneChangeList); return geneChangeList; } static void jsonWriteBranchAttrs(struct jsonWrite *jw, struct phyloTree *node, struct geneInfo *geneInfoList, struct seqWindow *gSeqWin) /* Write mutations (if any). If node is not a leaf, write label for mutations at this node. */ { if (node->priv != NULL) { struct singleNucChange *sncList = node->priv; struct slPair *geneAaMutations = getAaMutations(sncList, geneInfoList, gSeqWin); jsonWriteObjectStart(jw, "branch_attrs"); if (node->numEdges > 0) { jsonWriteObjectStart(jw, "labels"); struct singleNucChange *snc = sncList; struct dyString *dy = dyStringCreate("%c%d%c", snc->parBase, snc->chromStart+1, snc->newBase); for (snc = sncList->next; snc != NULL; snc = snc->next) dyStringPrintf(dy, ",%c%d%c", snc->parBase, snc->chromStart+1, snc->newBase); jsonWriteString(jw, "nuc mutations", dy->string); dyStringClear(dy); for (snc = sncList; snc != NULL; snc = snc->next) { char ref[2]; seqWindowCopy(gSeqWin, snc->chromStart, 1, ref, sizeof(ref)); if (snc->newBase == ref[0]) { dyStringAppendSep(dy, ","); dyStringPrintf(dy, "%c%d%c", snc->parBase, snc->chromStart+1, snc->newBase); } } jsonWriteString(jw, "back-mutations", dy->string); dyStringClear(dy); struct dyString *dyS = dyStringNew(0); struct slPair *geneAaMut; for (geneAaMut = geneAaMutations; geneAaMut != NULL; geneAaMut = geneAaMut->next) { struct slName *aaMut; for (aaMut = geneAaMut->val; aaMut != NULL; aaMut = aaMut->next) { dyStringAppendSep(dy, ","); dyStringPrintf(dy, "%s:%s", geneAaMut->name, aaMut->name); } if (sameString("S", geneAaMut->name)) { for (aaMut = geneAaMut->val; aaMut != NULL; aaMut = aaMut->next) { dyStringAppendSep(dyS, ","); dyStringPrintf(dyS, "%s:%s", geneAaMut->name, aaMut->name); } } } if (isNotEmpty(dy->string)) jsonWriteString(jw, "aa mutations", dy->string); if (isNotEmpty(dyS->string)) jsonWriteString(jw, "Spike mutations", dyS->string); dyStringFree(&dy); dyStringFree(&dyS); jsonWriteObjectEnd(jw); } jsonWriteObjectStart(jw, "mutations"); struct slPair *geneAaMut; for (geneAaMut = geneAaMutations; geneAaMut != NULL; geneAaMut = geneAaMut->next) { jsonWriteListStart(jw, geneAaMut->name); struct slName *aaMut; for (aaMut = geneAaMut->val; aaMut != NULL; aaMut = aaMut->next) jsonWriteString(jw, NULL, aaMut->name); jsonWriteListEnd(jw); } jsonWriteListStart(jw, "nuc"); struct singleNucChange *snc; for (snc = sncList; snc != NULL; snc = snc->next) jsonWriteStringf(jw, NULL, "%c%d%c", snc->parBase, snc->chromStart+1, snc->newBase); jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); // mutations jsonWriteObjectEnd(jw); // branch_attrs } } struct auspiceJsonInfo /* Collection of a bunch of things used when writing out auspice JSON for a subtree, so the * recursive function doesn't need a dozen args. */ { struct jsonWrite *jw; struct slName *subtreeUserSampleIds; // Subtree node names for user samples (not from big tree) struct geneInfo *geneInfoList; // Transcript seq & alignment for predicting AA change struct seqWindow *gSeqWin; // Reference genome seq for predicting AA change struct hash *sampleMetadata; // Sample metadata for decorating tree struct hash *sampleUrls; // URLs for samples, if applicable int nodeNum; // For generating sequential node ID (in absence of name) char *source; // Source of non-user sequences in tree (GISAID or public) }; static int cmpstringp(const void *p1, const void *p2) /* strcmp on pointers to strings, as in 'man qsort' but tolerate NULLs */ { char *s1 = *(char * const *)p1; char *s2 = *(char * const *)p2; if (s1 && s2) return strcmp(s1, s2); else if (s1 && !s2) return 1; else if (s2 && !s1) return -1; return 0; } static char *majorityMaybe(char *array[], int arraySize) /* Sort array and if a majority of its values are the same then return that value; otherwise NULL. */ { if (arraySize < 1) return NULL; qsort(array, arraySize, sizeof array[0], cmpstringp); char *maxRunVal = array[0]; int runLength = 1, maxRunLength = 1; int i; for (i = 1; i < arraySize; i++) { if (sameOk(array[i], array[i-1])) { runLength++; if (runLength > maxRunLength) { maxRunLength = runLength; maxRunVal = array[i]; } } else runLength = 1; } return (maxRunLength > (arraySize >> 1)) ? maxRunVal : NULL; } static void rTreeToAuspiceJson(struct phyloTree *node, int depth, struct auspiceJsonInfo *aji, char **retUserOrOld, char **retNClade, char **retGClade, char **retLineage, char **retNCladeUsher, char **retLineageUsher) /* Write Augur/Auspice V2 JSON for tree. Enclosing object start and end are written by caller. */ { if (node->priv) { struct singleNucChange *sncList = node->priv; depth += slCount(sncList); } boolean isUserSample = FALSE; if (node->ident->name) isUserSample = slNameInList(aji->subtreeUserSampleIds, node->ident->name); char *name = node->ident->name; struct sampleMetadata *met = name ? metadataForSample(aji->sampleMetadata, name) : NULL; if (name) jsonWriteString(aji->jw, "name", name); else jsonWriteStringf(aji->jw, "name", "NODE%d", aji->nodeNum++); jsonWriteBranchAttrs(aji->jw, node, aji->geneInfoList, aji->gSeqWin); if (node->numEdges > 0) { jsonWriteListStart(aji->jw, "children"); char *kidUserOrOld[node->numEdges]; char *kidNClade[node->numEdges]; char *kidGClade[node->numEdges]; char *kidLineage[node->numEdges]; char *kidNCladeUsher[node->numEdges]; char *kidLineageUsher[node->numEdges]; // Step through children in reverse order because nextstrain/Auspice draws upside-down. :) int i; for (i = node->numEdges - 1; i >= 0; i--) { jsonWriteObjectStart(aji->jw, NULL); rTreeToAuspiceJson(node->edges[i], depth, aji, &kidUserOrOld[i], &kidNClade[i], &kidGClade[i], &kidLineage[i], &kidNCladeUsher[i], &kidLineageUsher[i]); jsonWriteObjectEnd(aji->jw); } jsonWriteListEnd(aji->jw); if (retUserOrOld) *retUserOrOld = majorityMaybe(kidUserOrOld, node->numEdges); if (retNClade) *retNClade = majorityMaybe(kidNClade, node->numEdges); if (retGClade) *retGClade = majorityMaybe(kidGClade, node->numEdges); if (retLineage) *retLineage = majorityMaybe(kidLineage, node->numEdges); if (retNCladeUsher) *retNCladeUsher = majorityMaybe(kidNCladeUsher, node->numEdges); if (retLineageUsher) *retLineageUsher = majorityMaybe(kidLineageUsher, node->numEdges); } jsonWriteObjectStart(aji->jw, "node_attrs"); jsonWriteDouble(aji->jw, "div", depth); if (node->numEdges == 0) jsonWriteLeafNodeAttributes(aji->jw, name, met, isUserSample, aji->source, aji->sampleUrls, retUserOrOld, retNClade, retGClade, retLineage, retNCladeUsher, retLineageUsher); else if (retUserOrOld && retGClade && retLineage) jsonWriteBranchNodeAttributes(aji->jw, *retUserOrOld, *retNClade, *retGClade, *retLineage, *retNCladeUsher, *retLineageUsher); jsonWriteObjectEnd(aji->jw); } struct phyloTree *phyloTreeNewNode(char *name) /* Alloc & return a new node with no children. */ { struct phyloTree *node; AllocVar(node); AllocVar(node->ident); node->ident->name = cloneString(name); return node; } struct geneInfo *getGeneInfoList(char *bigGenePredFile, struct dnaSeq *refGenome) /* If config.ra has a source of gene annotations, then return the gene list. */ { struct geneInfo *geneInfoList = NULL; if (isNotEmpty(bigGenePredFile) && fileExists(bigGenePredFile)) { struct bbiFile *bbi = bigBedFileOpen(bigGenePredFile); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, 0, chromSize, 0, lm); for (bb = bbList; bb != NULL; bb = bb->next) { struct genePredExt *gp = genePredFromBigGenePred(chrom, bb); if (gp->strand[0] != '+') errAbort("getGeneInfoList: strand must be '+' but got '%s' for gene %s", gp->strand, gp->name); int txLen = 0; int ex; for (ex = 0; ex < gp->exonCount; ex++) txLen += (gp->exonEnds[ex] - gp->exonStarts[ex]); char *seq = needMem(txLen+1); int txOffset = 0; for (ex = 0; ex < gp->exonCount; ex++) { int exonLen = gp->exonEnds[ex] - gp->exonStarts[ex]; safencpy(seq+txOffset, txLen+1-txOffset, refGenome->dna+gp->exonStarts[ex], exonLen); txOffset += exonLen; } struct geneInfo *gi; AllocVar(gi); gi->psl = genePredToPsl((struct genePred *)gp, chromSize, txLen); gi->txSeq = newDnaSeq(seq, txLen, gp->name2); slAddHead(&geneInfoList, gi); } lmCleanup(&lm); bigBedFileClose(&bbi); } slReverse(&geneInfoList); return geneInfoList; } void treeToAuspiceJson(struct subtreeInfo *sti, char *db, struct geneInfo *geneInfoList, struct seqWindow *gSeqWin, struct hash *sampleMetadata, struct hash *sampleUrls, char *jsonFile, char *source) /* Write JSON for tree in Nextstrain's Augur/Auspice V2 JSON format * (https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json). */ { struct phyloTree *tree = sti->subtree; FILE *outF = mustOpen(jsonFile, "w"); fputs("{ \"version\": \"v2\", ", outF); writeAuspiceMeta(outF, sti->subtreeUserSampleIds, source); // The meta part is mostly constant & easier to just write out, but jsonWrite is better for the // nested tree structure. struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, "tree"); int nodeNum = 10000; // Auspice.us starting node number for newick -> json int depth = 0; // Add an extra root node because otherwise Auspice won't draw branch from big tree root to subtree struct phyloTree *root = phyloTreeNewNode("wrapper"); phyloAddEdge(root, tree); tree = root; struct auspiceJsonInfo aji = { jw, sti->subtreeUserSampleIds, geneInfoList, gSeqWin, sampleMetadata, sampleUrls, nodeNum, source }; rTreeToAuspiceJson(tree, depth, &aji, NULL, NULL, NULL, NULL, NULL, NULL); jsonWriteObjectEnd(jw); fputs(jw->dy->string, outF); jsonWriteFree(&jw); fputs("}", outF); carefulClose(&outF); }