3e968a25a2e9635f916fb3eeac0b3e2147cfba7c angie Mon Jun 28 08:43:35 2021 -0700 Add links to outbreak.info for lineages in results table & details. diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h index b2a803c..64391d4 100644 --- src/hg/hgPhyloPlace/phyloPlace.h +++ src/hg/hgPhyloPlace/phyloPlace.h @@ -1,223 +1,224 @@ /* Place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program. */ #ifndef _PHYLO_PLACE_H_ #define _PHYLO_PLACE_H_ #include "common.h" #include "dnaseq.h" #include "hash.h" #include "linefile.h" #include "parsimonyProto.h" #include "phyloTree.h" #include "seqWindow.h" #include "trashDir.h" #define PHYLOPLACE_DATA_DIR "hgPhyloPlaceData" // Allow users to upload a lot of sequences, but put limits on how much detail we'll show and // how many custom tracks we'll create. #define MAX_SUBTREE_BUTTONS 5 #define MAX_SEQ_DETAILS 100 #define MAX_SUBTREE_CTS 10 // For usher's -K option (single subtree): #define SINGLE_SUBTREE_SIZE "1000" #define NEXTSTRAIN_DRAG_DROP_DOC "https://docs.nextstrain.org/projects/auspice/en/latest/advanced-functionality/drag-drop-csv-tsv.html" +#define OUTBREAK_INFO_URLBASE "https://outbreak.info/situation-reports?pango=" struct treeChoices /* Phylogenetic tree versions for the user to choose from. */ { char **protobufFiles; // Mutation annotated tree files in protobuf format for UShER char **metadataFiles; // Sample metadata a la GISAID's nextmeta download option char **sources; // GISAID or public char **descriptions; // Menu labels to describe the options to the user char **aliasFiles; // Two-column files associating IDs/aliases with full tree names int count; // Number of choices (and size of each array) }; struct seqInfo /* User sequences, alignments and statistics */ { struct seqInfo *next; struct dnaSeq *seq; // Uploaded sequence struct psl *psl; // Alignment to reference (if FASTA uploaded) struct singleNucChange *sncList; // SNVs in seq struct singleNucChange *maskedSncList; // SNVs that were masked (not used for placement) struct slRef *maskedReasonsList; // Reason (from Problematic Sites) for masking each SNV uint nCountStart; // #Ns at beginning of seq uint nCountMiddle; // #Ns not at beginning or end of seq uint nCountEnd; // #Ns at end of seq uint ambigCount; // # ambiguous IUPAC bases char *insRanges; // ranges and sequences inserted into reference char *delRanges; // ranges and sequences deleted from reference uint insBases; // total #bases inserted into reference uint delBases; // total #bases deleted from reference }; struct variantPathNode /* A list of these gives a path from phylo tree root to some node (usually user seq leaf). */ { struct variantPathNode *next; char *nodeName; // Either a numeric internal node ID or the user seq name struct singleNucChange *sncList; // One or more single nucleotide changes associated with node }; struct bestNodeInfo { struct bestNodeInfo *next; char *name; // Node name struct variantPathNode *variantPath; // Mutations assigned to nodes along path from root->node boolean isSibling; // Placement would be as sibling of node (not child) }; struct baseVal /* List of imputed base positions and values */ { struct baseVal *next; int chromStart; // 0-based position char *val; // nucleotide base(s) }; struct placementInfo /* Info about a sample's mutations and placement in the phylo tree */ { char *sampleId; // Sample name from FASTA or VCF header struct slName *sampleMuts; // Differences with the reference genome struct variantPathNode *variantPath; // Mutations assigned to nodes along path from root struct bestNodeInfo *bestNodes; // Other nodes identified as equally parsimonious struct baseVal *imputedBases; // Ambiguous bases imputed to ref/alt [ACGT] int parsimonyScore; // Parsimony cost of placing sample int bestNodeCount; // Number of equally parsimonious placements char *nextClade; // Nextstrain clade assigned by UShER char *pangoLineage; // Pango lineage assigned by UShER // Fields above are parsed out of usher result files; below are added on later. char *nearestNeighbor; // Nearest neighbor in phylogenetic tree/NULL if not found char *neighborLineage; // Lineage of nearest neighbor/NULL if not found }; struct subtreeInfo /* Parsed subtree from usher and derivative products. */ { struct subtreeInfo *next; struct tempName *subtreeTn; // Newick file from usher (may have condensed nodes) struct phyloTree *subtree; // Parsed subtree (#*** with annotated muts? shoudl we?_ struct hash *subtreeIdToIx; // Map of subtree nodes to VCF output sample order struct slName *subtreeUserSampleIds; // List of user-uploaded samples in this subtree struct slName *subtreeNameList; // List of leaf names with nicer names for cond. nodes }; struct usherResults /* Tree+samples download file, sample placements, and subtrees parsed from usher output. */ { struct tempName *bigTreePlusTn; // Newick file: original tree plus user's samples struct hash *samplePlacements; // Info about each sample's placement in the tree struct subtreeInfo *singleSubtreeInfo; // Comprehensive subtree with all uploaded samples struct subtreeInfo *subtreeInfoList; // For each subtree: tree, file, node info etc. }; struct sampleMetadata /* Information about a virus sample. */ { char *strain; // Strain name, usually of the form Country/ArbitraryId/YYYY-MM-DD char *epiId; // GISAID EPI_ISL_[0-9]+ ID char *gbAcc; // GenBank accession char *date; // Sample collection date char *author; // Author(s) to credit char *nClade; // Nextstrain year-letter clade char *gClade; // GISAID amino acid change clade char *lineage; // Pangolin lineage char *country; // Country in which sample was collected char *division; // Administrative division in which sample was collected (country or state) char *location; // Location in which sample was collected (city) char *countryExp; // Country in which host was exposed to virus char *divExp; // Administrative division in which host was exposed to virus char *origLab; // Originating lab char *subLab; // Submitting lab char *region; // Continent on which sample was collected }; struct geneInfo /* Information sufficient to determine whether a genome change causes a coding change. */ { struct geneInfo *next; struct psl *psl; // Alignment of transcript to genome struct dnaSeq *txSeq; // Transcript sequence }; struct tempName *vcfFromFasta(struct lineFile *lf, char *db, struct dnaSeq *refGenome, boolean *informativeBases, struct slName **maskSites, struct slName **retSampleIds, struct seqInfo **retSeqInfo, struct slPair **retFailedSeqs, struct slPair **retFailedPsls, int *pStartTime); /* Read in FASTA from lf and make sure each item has a reasonable size and not too high * percentage of N's. Align to reference, extract SNVs from alignment, and save as VCF * with sample genotype columns. */ struct usherResults *runUsher(char *usherPath, char *usherAssignmentsPath, char *vcfFile, int subtreeSize, struct slName *userSampleIds, struct hash *condensedNodes, int *pStartTime); /* Open a pipe from Yatish Turakhia's usher program, save resulting big trees and * subtrees to trash files, return list of slRef to struct tempName for the trash files * and parse other results out of stderr output. */ struct usherResults *runMatUtilsExtractSubtrees(char *matUtilsPath, char *protobufPath, int subtreeSize, struct slName *sampleIds, struct hash *condensedNodes, int *pStartTime); /* Open a pipe from Yatish Turakhia and Jakob McBroome's matUtils extract to extract subtrees * containing sampleIds, save resulting subtrees to trash files, return subtree results. * Caller must ensure that sampleIds are names of leaves in the protobuf tree. */ 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 geneInfo *getGeneInfoList(char *bigGenePredFile, struct dnaSeq *refGenome); /* If config.ra has a source of gene annotations, then return the gene list. */ 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 tempName *writeCustomTracks(struct tempName *vcfTn, struct usherResults *ur, struct slName *sampleIds, struct phyloTree *bigTree, char *source, int fontHeight, struct phyloTree **retSampleTree, int *pStartTime); /* Write one custom track per subtree, and one custom track with just the user's uploaded samples. */ struct sampleMetadata *metadataForSample(struct hash *sampleMetadata, char *sampleId); /* Look up sampleId in sampleMetadata, by accession if sampleId seems to include an accession. */ struct phyloTree *phyloPruneToIds(struct phyloTree *node, struct slName *sampleIds); /* Prune all descendants of node that have no leaf descendants in sampleIds. */ char *phyloPlaceDbSetting(char *db, char *settingName); /* Return a setting from hgPhyloPlaceData/<db>/config.ra or NULL if not found. */ char *phyloPlaceDbSettingPath(char *db, char *settingName); /* Return path to a file named by a setting from hgPhyloPlaceData/<db>/config.ra, * or NULL if not found. (Append hgPhyloPlaceData/<db>/ to the beginning of relative path) */ struct treeChoices *loadTreeChoices(char *db); /* If <db>/config.ra specifies a treeChoices file, load it up, else return NULL. */ void reportTiming(int *pStartTime, char *message); /* Print out a report to stderr of how much time something took. */ boolean hgPhyloPlaceEnabled(); /* Return TRUE if hgPhyloPlace is enabled in hg.conf and db wuhCor1 exists. */ char *phyloPlaceSamples(struct lineFile *lf, char *db, char *defaultProtobuf, boolean doMeasureTiming, int subtreeSize, int fontHeight, boolean *retSuccess); /* Given a lineFile that contains either FASTA, VCF, or a list of sequence names/ids: * If FASTA/VCF, then prepare VCF for usher; if that goes well then run usher, report results, * make custom track files and return the top-level custom track file. * If list of seq names/ids, then attempt to find their full names in the protobuf, run matUtils * to make subtrees, show subtree results, and return NULL. Set retSuccess to TRUE if we were * able to get at least some results for the user's input. */ #endif //_PHYLO_PLACE_H_