4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/hgGene/otherOrgs.c src/hg/hgGene/otherOrgs.c index 5ed612e..98238fa 100644 --- src/hg/hgGene/otherOrgs.c +++ src/hg/hgGene/otherOrgs.c @@ -1,465 +1,465 @@ /* otherOrgs.c - Handle other species homolog section. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "dystring.h" #include "hui.h" #include "web.h" #include "hdb.h" #include "axt.h" #include "hgGene.h" struct otherOrg /* Links involving another organism. */ { struct otherOrg *next; /* Next in list. */ double priority; /* Order to print in. */ char *name; /* Symbolic name. */ char *shortLabel; /* Short human-readable label. */ char *idSql; /* SQL to create ID. */ char *idToProtIdSql;/* Convert from id to protein ID. */ char *otherIdSql; /* Convert from our id to other database ID. */ char *otherIdSql2; /* Try this if first otherIdSql doesn't work. */ char *genomeUrl; /* URL of genome browser link. */ char *sorterUrl; /* URL of gene sorter link. */ char *geneUrl; /* URL of hgGene link */ char *otherUrl; /* URL of other link. */ char *otherName; /* Name of other link. */ char *db; /* Other organism specific database. */ char *pepTable; /* Table in db peptides live in. */ char *geneTable; /* Table in db genes live in. */ }; static int otherOrgCmpPriority(const void *va, const void *vb) /* Compare to sort otherOrgs based on priority. */ { const struct otherOrg *a = *((struct otherOrg **)va); const struct otherOrg *b = *((struct otherOrg **)vb); float dif = a->priority - b->priority; if (dif < 0) return -1; else if (dif > 0) return 1; else return 0; } static char *otherOrgRequiredField(struct hash *hash, char *name) /* Return required field in otherOrg hash. Squawk and die if it doesn't exist. */ { char *s = hashFindVal(hash,name); if (s == NULL) errAbort("Couldn't find %s field in %s in otherOrgs.ra", name, (char *)hashFindVal(hash, "name")); return s; } static char *otherOrgOptionalField(struct hash *hash, char *name) /* Return field in hash if it exists or NULL otherwise. */ { return hashFindVal(hash, name); } static struct otherOrg *getOtherOrgList(struct sqlConnection *conn, char *raFile) /* Get list of otherOrgs - starting with everything in .ra file, * and making sure any associated tables and databases exist. */ { struct hash *ra, *raList = readRa(raFile, NULL); struct otherOrg *otherOrgList = NULL, *otherOrg; for (ra = raList; ra != NULL; ra = ra->next) { if (otherOrgOptionalField(ra, "hide") == NULL) { if (checkDatabases(otherOrgOptionalField(ra, "databases")) && sqlTablesExist(conn, otherOrgOptionalField(ra, "tables"))) { AllocVar(otherOrg); otherOrg->priority = atof(otherOrgRequiredField(ra, "priority")); otherOrg->name = otherOrgRequiredField(ra, "name"); otherOrg->shortLabel = otherOrgRequiredField(ra, "shortLabel"); otherOrg->idSql = otherOrgRequiredField(ra, "idSql"); otherOrg->idToProtIdSql = otherOrgOptionalField(ra, "idToProtIdSql"); char *otherIdSql = otherOrgOptionalField(ra, "otherIdSql"); if (otherIdSql) otherOrg->otherIdSql = replaceChars(otherIdSql, "KNOWNDB",sqlGetDatabase(conn)); otherOrg->otherIdSql2 = otherOrgOptionalField(ra, "otherIdSql2"); otherOrg->genomeUrl = otherOrgOptionalField(ra, "genomeUrl"); otherOrg->sorterUrl = otherOrgOptionalField(ra, "sorterUrl"); otherOrg->geneUrl = otherOrgOptionalField(ra, "geneUrl"); otherOrg->otherUrl = otherOrgOptionalField(ra, "otherUrl"); otherOrg->otherName = otherOrgOptionalField(ra, "otherName"); otherOrg->db = otherOrgRequiredField(ra, "db"); otherOrg->pepTable = otherOrgOptionalField(ra, "pepTable"); otherOrg->geneTable = otherOrgOptionalField(ra, "geneTable"); slAddHead(&otherOrgList, otherOrg); } } } slSort(&otherOrgList, otherOrgCmpPriority); return otherOrgList; } static boolean otherOrgsExists(struct section *section, struct sqlConnection *conn, char *geneId) /* Return TRUE if necessary database exists and has something * on this one. */ { struct otherOrg *otherOrgList; otherOrgList = section->items = getOtherOrgList(conn, section->raFile); return otherOrgList != NULL; return FALSE; } static char *otherOrgId(struct otherOrg *otherOrg, struct sqlConnection *conn, char *geneId) /* Return gene ID in other organism or NULL if it doesn't exist. */ { if (geneId != NULL) { char query[256]; sqlSafef(query, sizeof(query), otherOrg->idSql, geneId); return sqlQuickString(conn, query); } else return NULL; } static char *otherOrgPositionFromDb(struct otherOrg *otherOrg, char *id) /* Get position of id from other organism database, if possible. */ { struct hTableInfo *hti = hFindTableInfo(otherOrg->db, NULL, otherOrg->geneTable); if (hti == NULL) return NULL; // table not found struct sqlConnection *conn = hAllocConn(otherOrg->db); char query[512]; sqlSafef(query, sizeof(query), "select concat(%s, ':', %s+1, '-', %s) from %s " "where %s = '%s'", hti->chromField, hti->startField, hti->endField, otherOrg->geneTable, hti->nameField, id); char *pos = sqlQuickString(conn, query); if (pos != NULL) { char posPlus[2048]; safef(posPlus, sizeof(posPlus), "%s&%s=%s&hgFind.matches=%s", pos, otherOrg->geneTable, hTrackOpenVis(sqlGetDatabase(conn), otherOrg->geneTable), id); hFreeConn(&conn); freez(&pos); return cloneString(posPlus); } else { hFreeConn(&conn); return NULL; } } static char *otherOrgPosition(struct otherOrg *otherOrg, struct sqlConnection *conn, char *geneId) /* Return position of gene ID in other organism or NULL if it doesn't exist; * also make sure that the gene track is visible, and id highlighted, in * hgTracks (the destination when this is used). */ { char *id = otherOrgId(otherOrg, conn, geneId); if (id != NULL) { if (otherOrg->db == NULL || otherOrg->geneTable == NULL || !sqlDatabaseExists(otherOrg->db)) return id; else return otherOrgPositionFromDb(otherOrg, id); } return NULL; } static char *otherOrgProteinId(struct otherOrg *otherOrg, struct sqlConnection *conn, char *geneId) /* Return protein ID in other organism or NULL if it doesn't exist. */ { char *otherId = otherOrgId(otherOrg, conn, geneId); char *protId = NULL; if (otherOrg->db != NULL && otherId != NULL && otherOrg->idToProtIdSql != NULL && sqlDatabaseExists(otherOrg->db)) { struct sqlConnection *conn = hAllocConn(otherOrg->db); char query[512]; sqlSafef(query, sizeof(query), otherOrg->idToProtIdSql, otherId); protId = sqlQuickString(conn, query); hFreeConn(&conn); } if (protId == NULL) { protId = otherId; otherId = NULL; } freez(&otherId); return protId; } static char *otherOrgExternalId(struct otherOrg *otherOrg, char *localId) /* Convert other organism UCSC id to external database ID. */ { char *otherId = NULL; if (localId != NULL) { if (otherOrg->otherIdSql && sqlDatabaseExists(otherOrg->db)) { struct sqlConnection *conn = hAllocConn(otherOrg->db); char query[512]; sqlSafef(query, sizeof(query), otherOrg->otherIdSql, localId); otherId = sqlQuickString(conn, query); if (otherId == NULL && otherOrg->otherIdSql2 != NULL) { sqlSafef(query, sizeof(query), otherOrg->otherIdSql2, localId); otherId = sqlQuickString(conn, query); } hFreeConn(&conn); } else otherId = cloneString(localId); } return otherId; } static void otherOrgPrintLink(struct otherOrg *otherOrg, char *label, char *missingLabel, boolean internalLink, char *otherId, char *urlFormat) /* If label and urlFormat exist then print up a link. Otherwise print n/a. */ { if (internalLink) webPrintLinkCellStart(); else webPrintLinkOutCellStart(); if (urlFormat != NULL && label != NULL) { if (otherId != NULL) { hPrintf("<A HREF=\""); hPrintf(urlFormat, otherId); if (internalLink) hPrintf("&db=%s", otherOrg->db); hPrintf("\""); hPrintf(" TARGET=_blank"); hPrintf(" class=\"toc\">"); hPrintf("%s", label); hPrintf("</A>"); } else { hPrintf("%s", missingLabel); } } else hPrintf(" "); webPrintLinkCellEnd(); } void otherOrgPepLink(struct otherOrg *otherOrg, char *command, char *label, char *id, struct sqlConnection *conn) /* Print link that will invoke self to work on other organism peptide. */ { boolean gotIt = FALSE; webPrintLinkCellStart(); if (id != NULL) { if (otherOrg->db != NULL && otherOrg->pepTable != NULL) { char dbTable[128]; safef(dbTable, sizeof(dbTable), "%s.%s", otherOrg->db, otherOrg->pepTable); if (sqlTableExists(conn, dbTable)) { struct sqlResult *sr; char **row; char query[256]; sqlSafef(query, sizeof(query), "select seq from %s where name = '%s'", dbTable, id); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { gotIt = TRUE; hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\">", geneCgi, cartSidUrlString(cart), command, "on", hggOtherPepTable, dbTable, hggOtherId, id); hPrintf("%s", label); hPrintf("</A>"); } sqlFreeResult(&sr); } } } if (!gotIt) hPrintf(" "); webPrintLinkCellEnd(); } static void otherOrgsPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print the otherOrgs section. */ { struct otherOrg *otherOrg, *otherOrgList = section->items; hPrintf( "Orthologies between human, mouse, and rat are computed by taking the " "best BLASTP hit, and filtering out non-syntenic hits. For " "more distant species reciprocal-best BLASTP hits are used. " "Note that the absence of an ortholog in the table below may " "reflect incomplete annotations in the other species rather than " "a true absence of the orthologous gene."); webPrintLinkTableStart(); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) webPrintLabelCell(otherOrg->shortLabel); hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *pos = otherOrgPosition(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Genome Browser", "No ortholog", TRUE, pos, otherOrg->genomeUrl); freeMem(pos); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Gene Details", " ", TRUE, id, otherOrg->geneUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); otherOrgPrintLink(otherOrg, "Gene Sorter", " ", TRUE, id, otherOrg->sorterUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgId(otherOrg, conn, geneId); id = otherOrgExternalId(otherOrg, id); otherOrgPrintLink(otherOrg, otherOrg->otherName, " ", FALSE, id, otherOrg->otherUrl); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgProteinId(otherOrg, conn, geneId); otherOrgPepLink(otherOrg, hggDoOtherProteinSeq, "Protein Sequence", id, conn); freeMem(id); } hPrintf("</TR>\n<TR>"); for (otherOrg = otherOrgList; otherOrg != NULL; otherOrg = otherOrg->next) { char *id = otherOrgProteinId(otherOrg, conn, geneId); otherOrgPepLink(otherOrg, hggDoOtherProteinAli, "Alignment", id, conn); freeMem(id); } webPrintLinkTableEnd(); } struct section *otherOrgsSection(struct sqlConnection *conn, struct hash *sectionRa) /* Create otherOrgs section. */ { struct section *section = sectionNew(sectionRa, "otherOrgs"); section->exists = otherOrgsExists; section->print = otherOrgsPrint; section->raFile = "otherOrgs.ra"; return section; } void doOtherProteinSeq(struct sqlConnection *conn, char *homologName) /* Put up page that displays protein sequence from other organism. */ { char *table = cartString(cart, hggOtherPepTable); char *id = cartString(cart, hggOtherId); char name[256]; safef(name, sizeof(name), "%s homolog", homologName); showSeqFromTable(conn, id, name, table); } static bioSeq *getSeq(struct sqlConnection *conn, char *table, char *id) /* Get sequence from table. */ { char query[512]; struct sqlResult *sr; char **row; bioSeq *seq = NULL; sqlSafef(query, sizeof(query), "select seq from %s where name = '%s'", table, id); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { AllocVar(seq); seq->name = cloneString(id); seq->dna = cloneString(row[0]); seq->size = strlen(seq->dna); } sqlFreeResult(&sr); return seq; } void doOtherProteinAli(struct sqlConnection *conn, char *localId, char *localName) /* Put up page that shows alignment between this protein sequence * and other species. */ { char *otherTable = cartString(cart, hggOtherPepTable); char *otherId = cartString(cart, hggOtherId); char *localTable = genomeSetting("knownGenePep"); bioSeq *localSeq = getSeq(conn, localTable, localId); bioSeq *otherSeq = getSeq(conn, otherTable, otherId); if (localSeq != NULL && otherSeq != NULL) { struct axtScoreScheme *ss = axtScoreSchemeProteinDefault(); if (axtAffineSmallEnough(localSeq->size, otherSeq->size)) { struct axt *axt = axtAffine(localSeq, otherSeq, ss); hPrintf("<TT><PRE>"); if (axt != NULL) { printf("ID (including gaps) %3.1f%%, coverage (of both) %3.1f%%, score %d\n", axtIdWithGaps(axt)*100, axtCoverage(axt, localSeq->size, otherSeq->size)*100, axt->score); printf("Alignment between %s (top %s %daa) and\n", localName, localSeq->name, localSeq->size); printf("%s homolog (bottom %s %daa)\n", otherTable, otherSeq->name, otherSeq->size); printf("\n"); axtPrintTraditional(axt, 60, ss, stdout); axtFree(&axt); } else { printf("%s and %s don't align\n", localSeq->name, otherSeq->name); } hPrintf("</PRE></TT>"); } else { printf("Sorry, %s (%d amino acids) and %s (%d amino acids) are too big to align", localSeq->name, localSeq->size, otherSeq->name, otherSeq->size); } } else { warn("Couldn't get sequences, database out of sync?"); } }