void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Public Sessions");
/* Not in a form; can't use cartSaveSession() to set up an hgsid input */
printf ("<script>var common = {hgsid:\"%s\"};</script>\n", cartSessionId(cart));
jsIncludeDataTablesLibs();
printf("<p>Sessions allow users to save snapshots of the Genome Browser "
"and its current configuration, including displayed tracks, position, "
"and custom track data. The Public Sessions tool allows users to easily "
"share those sessions that they deem interesting with the rest of the "
"world's researchers. You can add your own sessions to this list by "
"checking the appropriate box on the "
"<a href=\"../cgi-bin/hgSession?%s\">Session Management</a> page.</p>\n"
"<p>See the "
"<a href=\"../goldenPath/help/hgSessionHelp.html\">Sessions User's Guide</a> "
"for more information.\n</p>", cartSidUrlString(cart));
showGalleryTab();
cartWebEnd();
}
static char *getDbForGenome(char *genome, struct cart *cart)
/*
Function to find the default database for the given Genome.
It looks in the cart first and then, if that database's Genome matches the
passed-in Genome, returns it. If the Genome does not match, it returns the default
database that does match that Genome.
param Genome - The Genome for which to find a database
param cart - The cart to use to first search for a suitable database name
return - The database matching this Genome type
*/
{
char *retDb = cartUsualString(cart, dbCgiName, NULL);
if ((retDb == NULL) || !hDbExists(retDb))
{
retDb = hDefaultDb();
}
/* If genomes don't match, then get the default db for that genome */
if (differentWord(genome, hGenome(retDb)))
{
retDb = hDefaultDbForGenome(genome);
}
return retDb;
}
int main(int argc, char *argv[])
{
optionInit(&argc, argv, optionSpecs);
char *db = optionVal("db", hDefaultDb());
if (argc < 2)
usage();
char *task = argv[1];
if (sameString(task, "parse"))
{
if (argc < 3)
usage();
char *trashFile = NULL;
char *inFile = argv[2];
if (argc > 3)
trashFile = argv[3];
parseCustomTracks(db, inFile, trashFile);
}
else if (sameString(task, "check"))
{
if (argc < 4)
usage();
char *outFile = argv[2];
char *expFile = argv[3];
checkCustomTracks(db, outFile, expFile);
}
else
usage();
return 0;
}
struct serverTable *findServer(char *db, boolean isTrans)
/* Return server for given database. Db can either be
* database name or description. */
{
if (trackHubDatabase(db))
{
struct serverTable *hubSt = trackHubServerTable(db, isTrans);
if (hubSt != NULL)
return hubSt;
errAbort("Cannot get blat server parameters for track hub with database %s\n", db);
}
static struct serverTable st;
struct sqlConnection *conn = hConnectCentral();
char query[256];
struct sqlResult *sr;
char **row;
char dbActualName[32];
/* If necessary convert database description to name. */
sqlSafef(query, sizeof(query), "select name from dbDb where name = '%s'", db);
if (!sqlExists(conn, query))
{
sqlSafef(query, sizeof(query), "select name from dbDb where description = '%s'", db);
if (sqlQuickQuery(conn, query, dbActualName, sizeof(dbActualName)) != NULL)
db = dbActualName;
}
/* Do a little join to get data to fit into the serverTable. */
sqlSafef(query, sizeof(query), "select dbDb.name,dbDb.description,blatServers.isTrans"
",blatServers.host,blatServers.port,dbDb.nibPath "
"from dbDb,blatServers where blatServers.isTrans = %d and "
"dbDb.name = '%s' and dbDb.name = blatServers.db",
isTrans, db);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
{
errAbort("Can't find a server for %s database %s. Click "
"<A HREF=\"/cgi-bin/hgBlat?%s&command=start&db=%s\">here</A> "
"to reset to default database.",
(isTrans ? "translated" : "DNA"), db,
cartSidUrlString(cart), hDefaultDb());
}
st.db = cloneString(row[0]);
st.genome = cloneString(row[1]);
st.isTrans = atoi(row[2]);
st.host = cloneString(row[3]);
st.port = cloneString(row[4]);
st.nibDir = hReplaceGbdbSeqDir(row[5], st.db);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return &st;
}
void usage()
/* explain usage and exit */
{
errAbort(
"customTrackTester - test program for custom tracks library\n\n"
"usage:\n"
" customTrackTester [options] task [args...]\n"
" where task/args can be:\n"
" parse inputFile [trashFile]\n"
" check outFile expectedFile\n"
"options:\n"
" -db=<db> - set database (defaults to %s)\n", hDefaultDb()
);
}
struct sqlConnection *dbConnect()
/* Get a connection do database specified in ~/.hg.conf */
{
struct sqlConnection *conn = NULL;
char *hdbHost = cfgOption("db.host");
char *hdbUser = cfgOption("db.user");
char *hdbPassword = cfgOption("db.password");
char *hdbDatabase = cfgOption("db.database");
if(hdbDatabase == NULL)
hdbDatabase = hDefaultDb();
if(hdbHost == NULL || hdbUser == NULL || hdbPassword == NULL)
errAbort("Cannot read in connection setting from configuration file.");
conn = sqlConnectRemote(hdbHost, hdbUser, hdbPassword, hdbDatabase);
return conn;
}
static void getUiState(struct cartJson *cj, struct hash *paramHash)
/* Write out JSON for hgGateway.js's uiState object using current cart settings. */
{
char *db = cartUsualString(cj->cart, "db", hDefaultDb());
char *position = cartUsualString(cart, "position", hDefaultPos(db));
char *hubUrl = NULL;
if (trackHubDatabase(db))
{
struct trackHub *hub = hubConnectGetHubForDb(db);
hubUrl = hub->url;
}
writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position);
// If cart already has a pix setting, pass that along; otherwise the JS will
// set pix according to web browser window width.
int pix = cartUsualInt(cj->cart, "pix", 0);
if (pix)
jsonWriteNumber(cj->jw, "pix", pix);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web plabel */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Try and get some simple D3 things running inside of Genome Browser web framework.");
printf("<script src=\"//cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min.js\"></script>");
printf("<script src=\"/js/d3pie.min.js\"></script>");
struct slPair *data= slPairNew("A","100");
slPairAdd(&data, "B", "10");
slPairAdd(&data, "C", "1");
slReverse(&data);
printf("<div id=\"pieChart1\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Subtitle");
printf("</div>\n");
slPairAdd(&data, "D", "10");
printf("<div id=\"pieChart2\">\n");
drawPrettyPieGraph(data, "pieChart1", "A new title", "cool subtitle!");
printf("</div>\n");
slPairAdd(&data, "W", "15");
printf("<div id=\"pieChart3\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Testing out what a much longer subtitle will look like... How many characters can I put here?");
printf("</div>\n");
slPairAdd(&data, "Z", "30");
printf("<div id=\"pieChart4\">\n");
drawPrettyPieGraph(data, "pieChart1", "How do much largers titles look?", "Subtitle");
printf("</div>\n");
printf("<style>\npieChart1{\n align:center;} </style>");
#ifdef SOON
drawPieGraph(data);
drawPieGraph(data);
slPairAdd(&data, "E", "15");
drawPieGraph(data);
slPairAdd(&data, "F", "25");
drawPieGraph(data);
slPairAdd(&data, "G", "50");
drawPieGraph(data);
#endif /* SOON */
cartWebEnd();
}
int main(int argc, char *argv[])
{
struct sqlConnection *conn, *conn2;
char query2[256];
struct sqlResult *sr2;
char **row2;
char cond_str[255];
char *proteinDatabaseName;
FILE *o1, *o2, *o3;
FILE *fh[23];
char temp_str[1000];;
char *accession;
char *aaSeq;
char *chp;
int i, j, len;
int ihi, ilow;
char *answer;
char *protDisplayId;
int aaResCnt[30];
char aaAlphabet[30];
int aaResFound;
float fvalue1, fvalue2;
float p1, p2;
int icnt, jcnt;
char *taxon;
char *database;
int sortedCnt;
if (argc != 4) usage();
strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB");
proteinDatabaseName = argv[1];
taxon = argv[2];
database = argv[3];
o2 = mustOpen("pbResAvgStd.tab", "w");
for (i=0; i<20; i++)
{
safef(temp_str, sizeof(temp_str), "%c.txt", aaAlphabet[i]);
fh[i] = mustOpen(temp_str, "w");
}
conn = hAllocConn(hDefaultDb());
conn2 = hAllocConn(hDefaultDb());
safef(query2, sizeof(query2), "select proteinID from %s.knownGene;", database);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
icnt = 0;
jcnt = 0;
for (j=0; j<MAXRES; j++)
{
sumJ[j] = 0;
}
while (row2 != NULL)
{
protDisplayId = row2[0];
safef(cond_str, sizeof(cond_str), "val='%s'", protDisplayId);
accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
if (accession == NULL)
{
safef(cond_str, sizeof(cond_str), "acc='%s'", protDisplayId);
accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);
if (accession == NULL)
{
verbose(2, "'%s' not found.\n", protDisplayId);
goto skip;
}
}
safef(cond_str, sizeof(cond_str), "accession='%s'", accession);
answer = sqlGetField("proteins040115", "spXref2", "biodatabaseID", cond_str);
if (answer == NULL)
{
/* this protein might be a variant splice protein, and then it won't be in spXref2 */
goto skip;
}
if (answer[0] != '1')
{
/* printf("%s not in SWISS-PROT\n", protDisplayId);fflush(stdout); */
goto skip;
}
safef(cond_str, sizeof(cond_str), "acc='%s'", accession);
aaSeq = sqlGetField(proteinDatabaseName, "protein", "val", cond_str);
if (aaSeq == NULL)
{
printf("Can't find peptide sequence for %s, exiting ...\n", protDisplayId);
fflush(stdout);
exit(1);
}
len = strlen(aaSeq);
if (len < 100) goto skip;
lenDouble = (double)len;
for (j=0; j<MAXRES; j++)
{
aaResCnt[j] = 0;
}
chp = aaSeq;
for (i=0; i<len; i++)
{
aaResFound = 0;
for (j=0; j<MAXRES; j++)
{
if (*chp == aaAlphabet[j])
{
aaResFound = 1;
aaResCnt[j] ++;
}
}
if (!aaResFound)
{
fprintf(stderr, "%c %d not a valid AA residue.\n", *chp, *chp);
}
chp++;
}
for (j=0; j<MAXRES; j++)
{
freq[icnt][j] = (double)aaResCnt[j]/lenDouble;
sumJ[j] = sumJ[j] + freq[icnt][j];
}
for (j=0; j<20; j++)
{
fprintf(fh[j], "%15.7f\t%s\n", freq[icnt][j], accession);
fflush(fh[j]);
}
icnt++;
if (icnt >= MAXN)
errAbort("Too many proteins - please set MAXN to be more than %d\n", MAXN);
skip:
row2 = sqlNextRow(sr2);
}
recordCnt = icnt;
recordCntDouble = (double)recordCnt;
for (j=0; j<20; j++)
{
carefulClose(&(fh[j]));
}
sqlFreeResult(&sr2);
hFreeConn(&conn);
hFreeConn(&conn2);
for (j=0; j<MAXRES; j++)
{
avg[j] = sumJ[j]/recordCntDouble;
}
for (j=0; j<20; j++)
{
sum = 0.0;
for (i=0; i<recordCnt; i++)
{
sum = sum + (freq[i][j] - avg[j]) * (freq[i][j] - avg[j]);
}
sigma[j] = sqrt(sum/(double)(recordCnt-1));
fprintf(o2, "%c\t%f\t%f\n", aaAlphabet[j], avg[j], sigma[j]);
}
carefulClose(&o2);
o1 = mustOpen("pbAnomLimit.tab", "w");
for (j=0; j<20; j++)
{
safef(temp_str, sizeof(temp_str), "cat %c.txt|sort|uniq > %c.srt", aaAlphabet[j], aaAlphabet[j]);
mustSystem(temp_str);
/* figure out how many unique entries */
safef(temp_str, sizeof(temp_str), "wc %c.srt > %c.tmp", aaAlphabet[j], aaAlphabet[j]);
mustSystem(temp_str);
safef(temp_str, sizeof(temp_str), "%c.tmp", aaAlphabet[j]);
o3 = mustOpen(temp_str, "r");
mustGetLine(o3, temp_str, 1000);
chp = temp_str;
while (*chp == ' ') chp++;
while (*chp != ' ') chp++;
*chp = '\0';
sscanf(temp_str, "%d", &sortedCnt);
safef(temp_str, sizeof(temp_str), "rm %c.tmp", aaAlphabet[j]);
mustSystem(temp_str);
/* cal hi and low cutoff threshold */
ilow = (int)((float)sortedCnt * 0.025);
ihi = (int)((float)sortedCnt * 0.975);
safef(temp_str, sizeof(temp_str), "%c.srt", aaAlphabet[j]);
o2 = mustOpen(temp_str, "r");
i=0;
for (i=0; i<ilow; i++)
{
mustGetLine(o2, temp_str, 1000);
}
sscanf(temp_str, "%f", &fvalue1);
mustGetLine(o2, temp_str, 1000);
sscanf(temp_str, "%f", &fvalue2);
p1 = (fvalue1 + fvalue2)/2.0;
for (i=ilow+1; i<ihi; i++)
{
mustGetLine(o2, temp_str, 1000);
}
sscanf(temp_str, "%f", &fvalue1);
mustGetLine(o2, temp_str, 1000);
sscanf(temp_str, "%f", &fvalue2);
p2 = (fvalue1 + fvalue2)/2.0;
carefulClose(&o2);
fprintf(o1, "%c\t%f\t%f\n", aaAlphabet[j], p1, p2);
fflush(stdout);
for (i=0; i<recordCnt; i++)
{
measure[i] = freq[i][j];
}
safef(temp_str, sizeof(temp_str), "pbAaDist%c.tab", aaAlphabet[j]);
calDist(measure, recordCnt, 51, 0.0, 0.005, temp_str);
}
carefulClose(&o1);
return(0);
}
int main(int argc, char *argv[])
{
struct sqlConnection *conn2, *conn3;
char query2[256];
struct sqlResult *sr2;
char **row2;
char *proteinDataDate;
FILE *o2;
char *entrez;
char *chp;
char *hgncId, *name, *symbol, *refSeqIds, *uniProt;
int j;
char *locusType;
char *refseq;
boolean gotRefseq;
if (argc != 2) usage();
proteinDataDate = argv[1];
o2 = fopen("j.dat", "w");
conn2= hAllocConn(hDefaultDb());
conn3= hAllocConn(hDefaultDb());
sprintf(query2,
"select hgncId, symbol, name, refSeqMapped, refSeqIds, uniProt, entrezMapped, locusType from proteins%s.hgnc where status not like '%cWithdrawn%c'",
proteinDataDate, '%', '%');
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
j=0;
hgncId = row2[j];j++;
symbol = row2[j];j++;
name = row2[j];j++;
refseq = row2[j];j++;
refSeqIds = row2[j];j++;
uniProt = row2[j];j++;
entrez = row2[j];j++;
locusType = row2[j];j++;
chp = strstr(hgncId, "HGNC:");
hgncId = chp+5;
gotRefseq = FALSE;
/* process refSeqMapped first */
if (!sameWord(refseq, ""))
{
fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
gotRefseq = TRUE;
}
/* process refSeqIds next */
chp = strstr(refSeqIds, ",");
if (chp != NULL)
{
*chp = '\0';
while (chp != NULL)
{
fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
chp++;
while (*chp == ' ') chp++;
refseq = chp;
chp = strstr(refseq, ",");
if (chp != NULL) *chp = '\0';
}
fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
gotRefseq = TRUE;
}
else
{
if (!sameWord(refseq,""))
{
fprintf(o2, "%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
}
else
{
/* output the record if no RefSeq in either refSeqIds or refSeqMapped */
if (!gotRefseq)
{
fprintf(o2,
"%s\t%s\t%s\t%s\t%s\t%s\n", symbol, refseq, uniProt, hgncId, entrez, name);
}
}
}
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
hFreeConn(&conn2);
fclose(o2);
mustSystem("cat j.dat |sort -u >hgncXref.tab");
return(0);
}
void getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome,
char **retClade, struct hash *oldVars)
/* Examine CGI and cart variables to determine which db, genome, or clade
* has been selected, and then adjust as necessary so that all three are
* consistent. Detect changes and reset db-specific cart variables.
* Save db, genome and clade in the cart so it will be consistent hereafter.
* The order of preference here is as follows:
* If we got a request that explicitly names the db, that takes
* highest priority, and we synch the organism to that db.
* If we get a cgi request for a specific organism then we use that
* organism to choose the DB. If just clade, go from there.
* In the cart only, we use the same order of preference.
* If someone requests an Genome we try to give them the same db as
* was in their cart, unless the Genome doesn't match.
*/
{
boolean gotClade = hGotClade();
*retDb = cgiOptionalString(dbCgiName);
*retGenome = cgiOptionalString(orgCgiName);
*retClade = cgiOptionalString(cladeCgiName);
/* phoneHome business */
phoneHome();
/* Was the database passed in as a cgi param?
* If so, it takes precedence and determines the genome. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
/* If no db was passed in as a cgi param then was the organism (a.k.a. genome)
* passed in as a cgi param?
* If so, the we use the proper database for that genome. */
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = getDbForGenome(*retGenome, cart);
*retGenome = hGenome(*retDb);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no cgi params passed in then we need to inspect the session */
else
{
*retDb = cartOptionalString(cart, dbCgiName);
*retGenome = cartOptionalString(cart, orgCgiName);
*retClade = cartOptionalString(cart, cladeCgiName);
/* If there was a db found in the session that determines everything. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = hDefaultDbForGenome(*retGenome);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no organism in the session then get the default db and organism. */
else
{
*retDb = hDefaultDb();
*retGenome = hGenome(*retDb);
}
}
*retDb = cloneString(*retDb);
*retGenome = cloneString(*retGenome);
*retClade = hClade(*retGenome);
/* Detect change of database and reset db-specific cart variables: */
if (oldVars)
{
char *oldDb = hashFindVal(oldVars, "db");
char *oldOrg = hashFindVal(oldVars, "org");
char *oldClade = hashFindVal(oldVars, "clade");
if ((!IS_CART_VAR_EMPTY(oldDb) && differentWord(oldDb, *retDb)) ||
(!IS_CART_VAR_EMPTY(oldOrg) && differentWord(oldOrg, *retGenome)) ||
(!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade)))
{
/* Change position to default -- unless it was passed in via CGI: */
if (cgiOptionalString("position") == NULL)
cartSetString(cart, "position", hDefaultPos(*retDb));
/* hgNear search term -- unless it was passed in via CGI: */
if (cgiOptionalString("near_search") == NULL)
cartRemove(cart, "near_search");
/* hgBlat results (hgUserPsl track): */
cartRemove(cart, "ss");
/* hgTables correlate: */
cartRemove(cart, "hgta_correlateTrack");
cartRemove(cart, "hgta_correlateTable");
cartRemove(cart, "hgta_correlateGroup");
cartRemove(cart, "hgta_correlateOp");
cartRemove(cart, "hgta_nextCorrelateTrack");
cartRemove(cart, "hgta_nextCorrelateTable");
cartRemove(cart, "hgta_nextCorrelateGroup");
cartRemove(cart, "hgta_nextCorrelateOp");
cartRemove(cart, "hgta_corrWinSize");
cartRemove(cart, "hgta_corrMaxLimitCount");
}
}
/* Save db, genome (as org) and clade in cart. */
cartSetString(cart, "db", *retDb);
cartSetString(cart, "org", *retGenome);
if (gotClade)
cartSetString(cart, "clade", *retClade);
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%u",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
"\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
"\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
"\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
"\t<TITLE>"
);
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
puts(
"<A NAME=\"TOP\"></A>" "\n"
"" "\n"
"<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart);
if(menuStr)
{
puts(menuStr);
}
if (endsWith(scriptName, "hgGateway") && geoMirrorEnabled())
{
// Show an opt-out alert if user is on a host to which user has been automatically redirected (just once, right after they have been redirected)
char *source = cgiOptionalString("source");
char *redirect = cgiOptionalString("redirect");
if (source != NULL && redirect != NULL && sameString(redirect, "auto"))
{
char *domain = cgiServerName();
char *port = cgiServerPort();
// We don't bother maintaining stuff in request URI, because it may contain items like hgsid and other host specific values
int newUriSize = 2048;
char *newUri = needMem(newUriSize);
safef(newUri, newUriSize, "http%s://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", source, port, domain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You've been redirected to your nearest mirror - %s"
"<idiv style=\"float:right;\">[x]</idiv>"
"</h3> "
"<ul style=\"margin:5px;\">"
"<li>Take me back to <a href=\"%s\">%s</a>"
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html\">What is this?</a></idiv>"
"</li>"
"</ul>"
"</div>"
"</TD></TR>\n"
, domain, newUri, source );
}
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
"<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
"<TR><TD COLSPAN=3>\n"
"<div id=firstSection>"
" <!--outer table is for border purposes-->\n"
" <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
"CELLPADDING='1'><TR><TD>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' "
"CELLPADDING='0'><TR><TD>\n"
" <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
);
htmlTextOut(textOutBuf);
puts(" </div></div>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
"<TR><TH HEIGHT=10></TH></TR>\n"
" <TR><TD WIDTH=10> </TD><TD>\n\n"
);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
} /* static void webStartWrapperDetailedInternal() */
int main(int argc, char *argv[])
{
struct sqlConnection *conn2, *conn3;
char query2[256], query3[256];
struct sqlResult *sr2, *sr3;
char **row2, **row3;
char *accession;
char *displayID;
char *division;
char *extDB;
char *extAC;
char *proteinDataDate;
char *genomeRelease;
FILE *o2, *o3;
char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd,
*exonCount, *exonStarts, *exonEnds;
char *bioDBID, *bioentryID;
if (argc != 3) usage();
proteinDataDate = argv[1];
genomeRelease = argv[2];
o2 = fopen("jj.dat", "w");
o3 = fopen("j.dat", "w");
conn2= hAllocConn(hDefaultDb());
conn3= hAllocConn(hDefaultDb());
sqlSafef(query2, sizeof query2, "select * from %sTemp.refGene;", genomeRelease);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
name = row2[0];
chrom = row2[1];
strand = row2[2];
txStart = row2[3];
txEnd = row2[4];
cdsStart = row2[5];
cdsEnd = row2[6];
exonCount = row2[7];
exonStarts= row2[8];
exonEnds = row2[9];
sqlSafef(query3, sizeof query3, "select * from proteins%s.spXref2 where extAC='%s' and extDB='EMBL';",
proteinDataDate, name);
sr3 = sqlMustGetResult(conn3, query3);
row3 = sqlNextRow(sr3);
while (row3 != NULL)
{
accession = row3[0];
displayID = row3[1];
division = row3[2];
extDB = row3[3];
extAC = row3[4];
bioentryID= row3[5];
bioDBID = row3[6];
if (! ( (strcmp(bioDBID, "1") == 0) ||
(strcmp(bioDBID, "2") == 0) ||
(strcmp(bioDBID, "3") == 0)
)
)
{
printf("non-recognized bioDB index %s encountered.\n", bioDBID);
printf("displayId=%s bioDBID=%s\n", displayID, bioDBID);
fflush(stdout);
exit(1);
}
fprintf(o2, "%s\n", displayID);
fprintf(o3, "%s\t%s\n", displayID, extAC);
row3 = sqlNextRow(sr3);
}
sqlFreeResult(&sr3);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
hFreeConn(&conn2);
hFreeConn(&conn3);
fclose(o2);
fclose(o3);
mustSystem("cat j.dat |sort|uniq >proteinMrna.tab");
mustSystem("cat jj.dat|sort|uniq >protein.lis");
mustSystem("rm j.dat");
mustSystem("rm jj.dat");
return(0);
}
int main(int argc, char *argv[])
{
struct sqlConnection *conn, *conn2;
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row, **row2;
FILE *o1;
char *proteomeDataDate;
char *uniprotDataDate;
char *bioDatabase, *bioentryID;
char *displayID;
char *accession;
char *extAC;
char *extDb;
char *division;
int iii;
char *extDbName[MAX_EXTDB];
int icnt;
int id;
char *val;
optionHash(&argc, argv);
if (argc != 3) usage();
uniprotDataDate = argv[1];
proteomeDataDate = argv[2];
o1 = mustOpen("temp_spXref2.dat", "w");
conn = hAllocConn(hDefaultDb());
conn2 = hAllocConn(hDefaultDb());
icnt =0;
/* first read in extDb table */
sqlSafef(query, sizeof(query), "select * from sp%s.extDb", uniprotDataDate);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
while (row != NULL)
{
icnt++;
if (icnt >= MAX_EXTDB)
{
errAbort("Too many extDBs - please set MAX_EXTDB to be more than %d\n", MAX_EXTDB);
}
id = atoi(row[0]);
val = row[1];
extDbName[id] = strdup(val);
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
iii=0;
/* Reuse the first 5 fields from the spXref3 table */
sqlSafef(query2, sizeof(query2),
"select accession, displayID, division, bioentryID, biodatabaseID from proteins%s.spXref3;",
proteomeDataDate);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
iii=0;
while (row2 != NULL)
{
accession = row2[0];
displayID = row2[1];
division = row2[2];
bioentryID = row2[3];
bioDatabase = row2[4];
sqlSafef(query, sizeof(query),
"select extAcc1, extDb.id from sp%s.extDb, sp%s.extDbRef where extDbRef.acc='%s' %s",
uniprotDataDate, uniprotDataDate, accession, "and extDb.id = extDbRef.extDb;");
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
while (row != NULL)
{
extAC = row[0];
extDb = extDbName[atoi(row[1])];
printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\n", accession, displayID, division,
extDb, extAC, bioentryID, bioDatabase);
iii++;
if ((iii%100000) == 0)
fprintf(stderr, "Processed %d records\n", iii);fflush(stderr);
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
row2 = sqlNextRow(sr2);
}
fclose(o1);
sqlFreeResult(&sr2);
hFreeConn(&conn);
hFreeConn(&conn2);
return(0);
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
webPragmasEtc();
printf("\t<TITLE>");
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
webStartSectionTables();
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart, db);
if(menuStr)
{
puts(menuStr);
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
webFirstSection(textOutBuf);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
errAbortSetDoContentType(FALSE);
} /* static void webStartWrapperDetailedInternal() */
char *getKnownGeneUrl(struct sqlConnection *conn, int geneId)
/* Given gene ID, try and find known gene on browser in same
* species. */
{
char query[256];
int taxon;
char *url = NULL;
char *genomeDb = NULL;
/* Figure out taxon. */
safef(query, sizeof(query),
"select taxon from gene where id = %d", geneId);
taxon = sqlQuickNum(conn, query);
genomeDb = hDbForTaxon(conn, taxon);
if (genomeDb != NULL)
{
/* Make sure known genes track exists - we may need
* to tweak this at some point for model organisms. */
safef(query, sizeof(query), "%s.knownToVisiGene", genomeDb);
if (!sqlTableExists(conn, query))
genomeDb = NULL;
}
/* If no db for that organism revert to human. */
if (genomeDb == NULL)
genomeDb = hDefaultDb();
safef(query, sizeof(query), "%s.knownToVisiGene", genomeDb);
if (sqlTableExists(conn, query))
{
struct dyString *dy = dyStringNew(0);
char *knownGene = NULL;
if (sqlCountColumnsInTable(conn, query) == 3)
{
dyStringPrintf(dy,
"select name from %s.knownToVisiGene where geneId = %d", genomeDb, geneId);
}
else
{
struct slName *imageList, *image;
safef(query, sizeof(query),
"select imageProbe.image from probe,imageProbe "
"where probe.gene=%d and imageProbe.probe=probe.id", geneId);
imageList = sqlQuickList(conn, query);
if (imageList != NULL)
{
dyStringPrintf(dy,
"select name from %s.knownToVisiGene ", genomeDb);
dyStringAppend(dy,
"where value in(");
for (image = imageList; image != NULL; image = image->next)
{
dyStringPrintf(dy, "'%s'", image->name);
if (image->next != NULL)
dyStringAppendC(dy, ',');
}
dyStringAppend(dy, ")");
slFreeList(&imageList);
}
}
if (dy->stringSize > 0)
{
knownGene = sqlQuickString(conn, dy->string);
if (knownGene != NULL)
{
dyStringClear(dy);
dyStringPrintf(dy, "../cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=none",
genomeDb, knownGene);
url = dyStringCannibalize(&dy);
}
}
dyStringFree(&dy);
}
freez(&genomeDb);
return url;
}
