void getAllSplices(char *database, FILE *f)
/* Write out table linking flybase genes with BDGP transcripts --
* unfortunately bdgpGeneInfo lacks -R* transcript/isoform identifiers,
* so strip those off of bdgpGene.name.
* This is not necessary with flyBaseGene/flyBase2004Xref where -R*'s
* are preserved.
*/
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256], **row;
struct geneAlt *altList = NULL, *alt;
struct hash *bdgpHash = newHash(16); /* Keyed by bdgp gene id. */
struct slName *n;
/* First build up list of all genes with flybase and bdgp ids. */
sqlSafef(query, sizeof(query), "select bdgpName,flyBaseId from bdgpGeneInfo");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
AllocVar(alt);
alt->bdgpName = cloneString(row[0]);
alt->fbName = cloneString(row[1]);
slAddHead(&altList, alt);
hashAdd(bdgpHash, alt->bdgpName, alt);
}
sqlFreeResult(&sr);
slReverse(&altList);
/* Now associate splicing variants. */
sqlSafef(query, sizeof(query), "select name from %s", geneTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *s = row[0];
char *e = rStringIn("-R", s);
int size = e ? (e - s) : strlen(s);
char bdgpGene[16];
if (size >= sizeof(bdgpGene))
errAbort("'%s' too big", s);
memcpy(bdgpGene, s, size);
bdgpGene[size] = 0;
alt = hashMustFindVal(bdgpHash, bdgpGene);
n = slNameNew(s);
slAddTail(&alt->isoformList, n);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
for (alt = altList; alt != NULL; alt = alt->next)
{
for (n = alt->isoformList; n != NULL; n = n->next)
fprintf(f, "%s\t%s\n", alt->fbName, n->name);
}
freeHash(&bdgpHash);
}
struct psl *getParentAligns(struct sqlConnection *conn, struct mappingInfo *mi, char **table)
{
struct ucscRetroInfo *pg = mi->pg;
struct psl *pslList = NULL;
char query[512];
if (startsWith("August",mi->geneSet))
{
if (hTableExists(database, "augustusXAli"))
{
*table = cloneString( "augustusXAli");
pslList = loadPslRangeT(*table, mi->seqId, pg->gChrom, pg->gStart, pg->gEnd);
}
else if (hTableExists(database, "augustusX"))
{
struct sqlResult *sr;
char **row;
int targetSize = 0;
*table = cloneString( "augustusX");
sqlSafef(query, sizeof(query), "select * from augustusX where chrom = '%s' and txEnd > %d and txStart < %d and name like '%s%%'",
pg->gChrom, pg->gStart, pg->gEnd , mi->seqId );
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+1);
sqlSafef(query, sizeof(query),
"select size from chromInfo where chrom = '%s' " , gp->chrom);
sqlFreeResult(&sr);
targetSize = sqlNeedQuickNum(conn, query) ;
pslList = pslFromGenePred(gp, targetSize);
}
}
}
else if (hTableExists(database, "all_mrna"))
{
char parent[255];
char *dotPtr ;
*table = cloneString( "all_mrna");
safef(parent, sizeof(parent), "%s",pg->name);
/* strip off version and unique suffix when looking for parent gene*/
dotPtr = rStringIn(".",parent) ;
if (dotPtr != NULL)
*dotPtr = '\0';
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
if (pslList == NULL)
{
*table = cloneString( "refSeqAli");
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
}
}
else
printf("no all_mrna table found<br>\n");
return pslList;
}
static char *doChopsAndUpper(struct joinerField *jf, char *id)
/* Return chopped version of id. (This may insert a zero into s).
* Also upper case it. */
{
struct slName *chop;
for (chop = jf->chopBefore; chop != NULL; chop = chop->next)
{
char *s = stringIn(chop->name, id);
if (s != NULL)
id = s + strlen(chop->name);
}
for (chop = jf->chopAfter; chop != NULL; chop = chop->next)
{
char *s = rStringIn(chop->name, id);
if (s != NULL)
*s = 0;
}
touppers(id);
return id;
}
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() */
static void doSeqAndExtFile(struct sqlConnection *conn, char *db, char *table)
{
int rc = 0;
char cmd[256];
char path[256];
char bedPath[256];
char gbdbPath[256];
char *fname=NULL;
struct dyString *dy = dyStringNew(0);
dyStringClear(dy);
dyStringPrintf(dy,
"select distinct concat('vgPrb_',e.id), e.seq"
" from vgPrb e join %s.%s v"
" left join %s.seq s on s.acc = v.qName"
" where concat('vgPrb_',e.id) = v.qName"
" and s.acc is NULL"
" order by e.id"
, db, table, db);
rc = sqlSaveQuery(conn, dy->string, "vgPrbExt.fa", TRUE);
verbose(1,"rc = %d = count of sequences for vgPrbExt.fa, to use with %s track %s\n",rc,db,table);
if (rc > 0) /* can set any desired minimum */
{
safef(bedPath,sizeof(bedPath),"/cluster/data/%s/bed/visiGene/",db);
if (!fileExists(bedPath))
{
safef(cmd,sizeof(cmd),"mkdir %s",bedPath);
verbose(1,"%s\n",cmd); system(cmd);
}
safef(gbdbPath,sizeof(gbdbPath),"/gbdb/%s/visiGene/",db);
if (!fileExists(gbdbPath))
{
safef(cmd,sizeof(cmd),"mkdir %s",gbdbPath);
verbose(1,"%s\n",cmd); system(cmd);
}
while(1)
{
int i=0;
safef(path,sizeof(path),"%svgPrbExt_AAAAAA.fa",bedPath);
char *c = rStringIn("AAAAAA",path);
srand( (unsigned)time( NULL ) );
for(i=0;i<6;++i)
{
*c++ += (int) 26 * (rand() / (RAND_MAX + 1.0));
}
if (!fileExists(path))
break;
}
safef(cmd,sizeof(cmd),"cp vgPrbExt.fa %s",path);
verbose(1,"%s\n",cmd); system(cmd);
fname = rStringIn("/", path);
++fname;
safef(cmd,sizeof(cmd),"ln -s %s %s%s",path,gbdbPath,fname);
verbose(1,"%s\n",cmd); system(cmd);
safef(cmd,sizeof(cmd),"hgLoadSeq %s %s%s", db, gbdbPath,fname);
verbose(1,"%s\n",cmd); system(cmd);
}
dyStringFree(&dy);
}
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() */
