e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/hgc/virusClick.c src/hg/hgc/virusClick.c index 55f15eb..19e8616 100644 --- src/hg/hgc/virusClick.c +++ src/hg/hgc/virusClick.c @@ -1,623 +1,626 @@ /* virusClick - hgc code for a prototype virus browser on the h1n1 genome */ +/* Copyright (C) 2013 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #include "common.h" #include "hgc.h" #include "virusClick.h" #include "hCommon.h" #include "hgConfig.h" #include "linefile.h" #include "dystring.h" #include "lsSnpPdbChimera.h" #include "jksql.h" #include "net.h" #include "trashDir.h" #include "htmshell.h" static void h1n1DownloadPdb(char *item, char *pdbUrl, struct tempName *tmpPdb) /* uncompress PDB to trash */ { int inFd = netOpenHttpExt(pdbUrl, "GET", NULL); int inFdRedir = 0; char *pdbUrlRedir = NULL; if (!netSkipHttpHeaderLinesHandlingRedirect(inFd, pdbUrl, &inFdRedir, &pdbUrlRedir)) errAbort("Unable to access predicted 3D structure file: %s", pdbUrl); if (pdbUrlRedir != NULL) { close(inFd); inFd = inFdRedir; freez(&pdbUrlRedir); } trashDirFile(tmpPdb, "hgct", item, ".pdb"); FILE *outFh = mustOpen(tmpPdb->forCgi, "w"); struct lineFile *inLf = lineFileDecompressFd(pdbUrl, TRUE, inFd); char *line; while (lineFileNext(inLf, &line, NULL)) { fputs(line, outFh); fputc('\n', outFh); } lineFileClose(&inLf); carefulClose(&outFh); } static void h1n1MkChimeraxTrashFullUrl(struct tempName *tmpPdb, char *fullUrl, int fullUrlSize) /* generate full URL for a chimerax file decompressed to trash */ { // FIXME: this is not generate (URL generation will not work on all web servers). // if this is kept, should address this. char *serverName = getenv("SERVER_NAME"); char *serverPort = getenv("SERVER_PORT"); char *scriptName = getenv("SCRIPT_NAME"); if ((serverName != NULL) && (serverPort != NULL) && (scriptName != NULL)) { // remote url safef(fullUrl, fullUrlSize, "http://%s", serverName); if (!sameString(serverPort, "80")) { safecat(fullUrl, fullUrlSize, ":"); safecat(fullUrl, fullUrlSize, serverPort); } safecat(fullUrl, fullUrlSize, scriptName); char *p = strrchr(fullUrl, '/'); if (p != NULL) *++p = '\0'; // drop cgi name, keeping directory safecat(fullUrl, fullUrlSize, tmpPdb->forHtml); } else { // local url safef(fullUrl, fullUrlSize, "file:///%s/%s", getCurrentDir(), tmpPdb->forHtml); } } static char *mkChimeraPyScript(char *scriptFile) /* create chimera python script from commands in scriptFile */ { struct dyString *buf = dyStringNew(0); dyStringAppend(buf, "from chimera import runCommand\n"); struct lineFile *lf = lineFileOpen(scriptFile, TRUE); char *line; while (lineFileNextReal(lf, &line)) dyStringPrintf(buf, "runCommand(\"%s\")\n", line); lineFileClose(&lf); return dyStringCannibalize(&buf); } static void mkChimerax(char *item, char *pdbUrl, char *scriptFile, struct tempName *chimerax) /* generate a chimerax file for downloading h1n1 PDB structure */ { // chimera doesn't handle compressed files via URL, so uncompress into the trash struct tempName tmpPdb; char usePdbUrl[PATH_LEN]; if (endsWith(pdbUrl, ".gz") || endsWith(pdbUrl, ".Z")) { h1n1DownloadPdb(item, pdbUrl, &tmpPdb); h1n1MkChimeraxTrashFullUrl(&tmpPdb, usePdbUrl, sizeof(usePdbUrl)); } else safecpy(usePdbUrl, sizeof(usePdbUrl), pdbUrl); char *pyScript = NULL; if (scriptFile != NULL) pyScript = mkChimeraPyScript(scriptFile); lsSnpPdbChimeraGenericLink(usePdbUrl, pyScript, "hgct", item, chimerax); freeMem(pyScript); } static void tempNameFromPrefix(struct tempName *name, struct tempName *prefix, char *suffix) /* build a tempName based on an existing tempName and a suffix */ { safecpy(name->forCgi, sizeof(name->forCgi), prefix->forCgi); safecat(name->forCgi, sizeof(name->forCgi), suffix); safecpy(name->forHtml, sizeof(name->forHtml), prefix->forHtml); safecat(name->forHtml, sizeof(name->forHtml), suffix); } static char *getH1n1StructDir() /* get location of h1n1 modeling directory */ { static char *dir = NULL; if (dir == NULL) { dir = cfgOption("gisaid.structDir"); if (dir == NULL) errAbort("gisaid.structDir not set in hg.conf"); } return dir; } static char *getH1n1StructUrl() /* get URL of h1n1 modeling directory */ { static char *url = NULL; if (url == NULL) { url = cfgOption("gisaid.structUrl"); if (url == NULL) errAbort("gisaid.structUrl not set in hg.conf"); } return url; } static boolean getH1n1Model(char *gene, char *pdbUrl) /* Find model PDB file URL, return false if does not exist. URL is * return in pdbUrl if it is not NULL */ { char relPath[PATH_LEN], pdbPath[PATH_LEN]; if (sameString(gene, "HA")) safef(relPath, sizeof(relPath), "%s/%s", gene, "consensus.uncleaved.D18-G519.pdb"); else if (sameString(gene, "NA")) safef(relPath, sizeof(relPath), "%s/%s", gene, "consensus.tetramer.V83-I467.pdb"); else return FALSE; if (pdbUrl != NULL) safef(pdbUrl, PATH_LEN, "%s/%s", getH1n1StructUrl(), relPath); safef(pdbPath, sizeof(pdbPath), "%s/%s", getH1n1StructDir(), relPath); return fileExists(pdbPath); } static void mkH1n1StructData(char *gene, char *idPairFile, char *highlightId, struct tempName *imageFile, struct tempName *chimeraScript) /* generate 3D structure files; difference highlighting is generate only idPairFile or * idPairFile, if specified, but not both. */ { struct tempName prefix; trashDirFile(&prefix, "hgct", gene, "tmp"); char idFile[PATH_LEN], idArg[PATH_LEN], logFile[PATH_LEN], cmd[2*PATH_LEN]; idArg[0] = '\0'; if ((idPairFile != NULL) || (highlightId != NULL)) { safef(idFile, sizeof(idFile), "%s.ids", prefix.forCgi); if (idPairFile != NULL) { // extract first column safef(cmd, sizeof(cmd), "cut -f 1 %s >%s", idPairFile, idFile); if (system(cmd) != 0) errAbort("extracting protein ids failed: %s", cmd); } else { FILE *fh = mustOpen(idFile, "w"); fprintf(fh, "%s\n", highlightId); carefulClose(&fh); } safef(idArg, sizeof(idArg), "--ids %s", idFile); } // dynamic_highlight.pl knows locations of model files safef(logFile, sizeof(logFile), "%s.log", prefix.forCgi); safef(cmd, sizeof(cmd), "%s/dynamic_highlight.pl --rasmol --chimera --protein %s --consensus 0602 %s --base %s >%s 2>&1", getH1n1StructDir(), gene, idArg, prefix.forCgi, logFile); if (system(cmd) != 0) errAbort("creation of 3D structure highlight files failed: %s", cmd); // output names are all predefined by script relative to prefix tempNameFromPrefix(imageFile, &prefix, "_highlight.jpg"); tempNameFromPrefix(chimeraScript, &prefix, "_highlight.cmd"); } static void showProtH1n1(char *item, char *geneSymbol) { char query2[256]; struct sqlResult *sr2; char **row2; struct sqlConnection *conn2 = hAllocConn(database); char *subjId, *dnaSeqId; char *aaSeqId= NULL; char *gene=NULL; char cond_str[256]; char *predFN; char *homologID; char *SCOPdomain; char *chain; char goodSCOPdomain[40]; int first = 1; float eValue; char *chp; int homologCount; int gotPDBFile = 0; sqlSafef(query2, sizeof(query2), "select subjId, dnaSeqId, aaSeqId, gene from gisaidXref where dnaSeqId='%s'", item); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { subjId = strdup(row2[0]); dnaSeqId = strdup(row2[1]); aaSeqId = strdup(row2[2]); gene = strdup(row2[3]); } else { errAbort("%s not found.", item); } sqlFreeResult(&sr2); printf("<H3>Protein Structure Analysis and Prediction</H3>"); printf("<B>Comparison to 1918 Flu Virus:</B> "); printf("<A HREF=\"%s/%s/%s/1918_%s.mutate", getH1n1StructUrl(), gene, aaSeqId, aaSeqId); printf("\" TARGET=_blank>%s</A><BR>\n", aaSeqId); printf("<B>Comparison to A H1N1 gene %s concensus:</B> ", gene); printf("<A HREF=\"%s/%s/%s/consensus_%s.mutate", getH1n1StructUrl(), gene, aaSeqId, aaSeqId); printf("\" TARGET=_blank>%s</A><BR>\n", aaSeqId); printf("<BR><B>3D Structure Prediction of %s concensus sequence (with variation of sequence %s highlighted):", geneSymbol, item); printf("<BR>PDB file:</B> "); char pdbUrl[PATH_LEN]; safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item); // Modeller stuff char modelPdbUrl[PATH_LEN]; if (getH1n1Model(gene, modelPdbUrl)) { struct tempName imageFile, chimeraScript, chimerax; mkH1n1StructData(gene, NULL, aaSeqId, &imageFile, &chimeraScript); mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax); printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n", modelPdbUrl, gene, chimerax.forHtml); printf("<TABLE>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml); printf("</TR>\n"); printf("</TABLE>\n"); } return; gotPDBFile = 0; sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s' and evalue <1.0e-5;", item); printf("<TABLE>\n"); printf("<TR><TD ALIGN=\"center\">Front</TD>\n"); printf("<TD ALIGN=\"center\">Top</TD>\n"); printf("<TD ALIGN=\"center\">Side</TD>\n"); printf("</TR>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view1_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view2_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view3_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("</TR>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view1_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view2_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view3_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("</TR>\n"); printf("</TABLE>\n"); printf("<BR><B>Detailed results of SAM-T02:</B> "); printf("<A HREF=\"%s/%s/summary.html", getH1n1StructUrl(), item); printf("\" TARGET=_blank>%s</A><BR>\n", item); /* by pass the following additional processing for now, until two necessary tables are built */ hFreeConn(&conn2); return; if (sqlGetField(database, "protHomolog", "proteinID", cond_str) != NULL) { sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", item); predFN = sqlGetField(database, "protPredFile", "predFileName", cond_str); if (predFN != NULL) { printf("<A HREF=\"../SARS/%s/", item); /* printf("%s.t2k.undertaker-align.pdb\">%s</A><BR>\n", item,item); */ printf("%s\">%s</A><BR>\n", predFN,item); gotPDBFile = 1; } } if (!gotPDBFile) { printf("No high confidence level structure prediction available for this sequence."); printf("<BR>\n"); } printf("<B>3D Structure of Close Homologs:</B> "); homologCount = 0; strcpy(goodSCOPdomain, "dummy"); conn2= hAllocConn(database); sqlSafef(query2, sizeof(query2), "select homologID,eValue,SCOPdomain,chain from sc1.protHomolog where proteinID='%s' and evalue <= 0.01;", item); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { while (row2 != NULL) { homologID = row2[0]; sscanf(row2[1], "%e", &eValue); SCOPdomain = row2[2]; chp = SCOPdomain+strlen(SCOPdomain)-1; while (*chp != '.') chp--; *chp = '\0'; chain = row2[3]; if (eValue <= 1.0e-10) strcpy(goodSCOPdomain, SCOPdomain); else { if (strcmp(goodSCOPdomain,SCOPdomain) != 0) goto skip; else if (eValue > 0.1) goto skip; } if (first) first = 0; else printf(", "); printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s", homologID); if (strlen(chain) >= 1) printf("\"TARGET=_blank>%s(chain %s)</A>", homologID, chain); else printf("\"TARGET=_blank>%s</A>", homologID); homologCount++; skip: row2 = sqlNextRow(sr2); } } hFreeConn(&conn2); sqlFreeResult(&sr2); if (homologCount == 0) printf("None<BR>\n"); printf("<BR><B>Details:</B> "); printf("<A HREF=\"../SARS/%s/summary.html", item); printf("\" TARGET=_blank>%s</A><BR>\n", item); htmlHorizontalLine(); } void showSAM_h1n1(char *item) { char query2[256]; struct sqlResult *sr2; char **row2; struct sqlConnection *conn2 = hAllocConn(database); char cond_str[256]; char *predFN; char *homologID; char *SCOPdomain; char *chain; char goodSCOPdomain[40]; int first = 1; float eValue; char *chp; int homologCount; int gotPDBFile = 0; printf("<H3>Protein Structure Analysis and Prediction by "); printf("<A HREF=\"http://www.soe.ucsc.edu/research/compbio/SAM_T02/sam-t02-faq.html\""); printf(" TARGET=_blank>SAM-T02</A></H3>\n"); printf("<B>Multiple Alignment:</B> "); printf("<A HREF=\"%s/%s/summary.html#alignment", getH1n1StructUrl(), item); printf("\" TARGET=_blank>%s</A><BR>\n", item); printf("<B>Secondary Structure Predictions:</B> "); printf("<A HREF=\"%s/%s/summary.html#secondary-structure", getH1n1StructUrl(), item); printf("\" TARGET=_blank>%s</A><BR>\n", item); printf("<B>3D Structure Prediction (PDB file):</B> "); char pdbUrl[PATH_LEN]; safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item); struct tempName chimerax; mkChimerax(item, pdbUrl, NULL, &chimerax); printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n", pdbUrl, item, chimerax.forHtml); gotPDBFile = 0; sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s' and evalue <1.0e-5;", item); printf("<TABLE>\n"); printf("<TR><TD ALIGN=\"center\">Front</TD>\n"); printf("<TD ALIGN=\"center\">Top</TD>\n"); printf("<TD ALIGN=\"center\">Side</TD>\n"); printf("</TR>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view1_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view2_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><img src=\"%s/%s/%s.undertaker-align.view3_200.jpg\"></TD>", getH1n1StructUrl(), item, item); printf("</TR>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view1_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view2_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("<TD ALIGN=\"center\"><A HREF=\"%s/%s/%s.undertaker-align.view3_500.jpg\">500x500</A></TD>", getH1n1StructUrl(), item, item); printf("</TR>\n"); printf("</TABLE>\n"); printf("<BR><B>Detailed results of SAM-T02:</B> "); printf("<A HREF=\"%s/%s/summary.html", getH1n1StructUrl(), item); printf("\" TARGET=_blank>%s</A><BR>\n", item); /* by pass the following additional processing for now, until two necessary tables are built */ hFreeConn(&conn2); return; if (sqlGetField(database, "protHomolog", "proteinID", cond_str) != NULL) { sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", item); predFN = sqlGetField(database, "protPredFile", "predFileName", cond_str); if (predFN != NULL) { printf("<A HREF=\"../SARS/%s/", item); /* printf("%s.t2k.undertaker-align.pdb\">%s</A><BR>\n", item,item); */ printf("%s\">%s</A><BR>\n", predFN,item); gotPDBFile = 1; } } if (!gotPDBFile) { printf("No high confidence level structure prediction available for this sequence."); printf("<BR>\n"); } printf("<B>3D Structure of Close Homologs:</B> "); homologCount = 0; strcpy(goodSCOPdomain, "dummy"); conn2= hAllocConn(database); sqlSafef(query2, sizeof(query2), "select homologID,eValue,SCOPdomain,chain from sc1.protHomolog where proteinID='%s' and evalue <= 0.01;", item); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); if (row2 != NULL) { while (row2 != NULL) { homologID = row2[0]; sscanf(row2[1], "%e", &eValue); SCOPdomain = row2[2]; chp = SCOPdomain+strlen(SCOPdomain)-1; while (*chp != '.') chp--; *chp = '\0'; chain = row2[3]; if (eValue <= 1.0e-10) strcpy(goodSCOPdomain, SCOPdomain); else { if (strcmp(goodSCOPdomain,SCOPdomain) != 0) goto skip; else if (eValue > 0.1) goto skip; } if (first) first = 0; else printf(", "); printf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s", homologID); if (strlen(chain) >= 1) printf("\"TARGET=_blank>%s(chain %s)</A>", homologID, chain); else printf("\"TARGET=_blank>%s</A>", homologID); homologCount++; skip: row2 = sqlNextRow(sr2); } } hFreeConn(&conn2); sqlFreeResult(&sr2); if (homologCount == 0) printf("None<BR>\n"); printf("<BR><B>Details:</B> "); printf("<A HREF=\"../SARS/%s/summary.html", item); printf("\" TARGET=_blank>%s</A><BR>\n", item); htmlHorizontalLine(); } void doH1n1Seq(struct trackDb *tdb, char *item) /* Show extra info for H1N1 Seq Annotations track. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; char *geneSymbol=NULL; genericHeader(tdb, item); sqlSafef(query, sizeof query, "select seqId, geneSymbol, strain, islId from h1n1SeqXref where seqId = '%s'", item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { char *seqId, *strain, *islId; seqId = row[0]; geneSymbol = row[1]; strain = row[2]; islId = row[3]; printf("<B>Sequence ID: %s</B> <BR>", seqId); printf("<B>Gene: %s</B> <BR>", geneSymbol); printf("<B>Strain: %s</B> <BR>", strain); printf("<B>Isolate: </B> "); printf("<A HREF=\"../cgi-bin/gisaidSample?hgs_sample=%s&submit=Go\">%s</A>", islId, islId); } htmlHorizontalLine(); //showSAM_h1n1(item); showProtH1n1(item, geneSymbol); htmlHorizontalLine(); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void doH1n1Gene(struct trackDb *tdb, char *item) /* Show details page for H1N1 Genes and Regions annotations track. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; char *chrom, *chromStart, *chromEnd; char *gene=NULL; genericHeader(tdb, item); gene = item; printf("<B>Gene: </B> %s\n<BR>", gene); sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from h1n1Gene where name='%s';", gene); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { chrom = row[0]; chromStart = row[1]; chromEnd = row[2]; printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, item); } sqlFreeResult(&sr); hFreeConn(&conn); htmlHorizontalLine(); printf("<H3>Protein Structure Analysis and Prediction</H3>"); printf("<B>3D Structure Prediction of consensus sequence (with variations of all selected sequences highlighted):"); printf("<BR>PDB file:</B> "); char pdbUrl[PATH_LEN]; safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item); // Modeller stuff char modelPdbUrl[PATH_LEN]; if (getH1n1Model(gene, modelPdbUrl)) { char *selectFile = cartOptionalString(cart, gisaidAaSeqList); struct tempName imageFile, chimeraScript, chimerax; mkH1n1StructData(gene, selectFile, NULL, &imageFile, &chimeraScript); mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax); printf("<A HREF=\"%s\" TARGET=_blank>%s</A>, view with <A HREF=\"%s\">Chimera</A><BR>\n", modelPdbUrl, gene, chimerax.forHtml); printf("<TABLE>\n"); printf("<TR>\n"); printf("<TD ALIGN=\"center\"><img src=\"%s\"></TD>", imageFile.forHtml); printf("</TR>\n"); printf("</TABLE>\n"); } htmlHorizontalLine(); printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); }