int main (int argc, char *argv[])
{
FILE* ftmp = NULL;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL)
return EXIT_FAILURE;
cgiInit();
cgiHeader("text/html");
if (argc == 3) {
GfrEntry *currGE;
Stringa buffer;
GfrPairCount *currGEPC;
GfrInterRead *currGIR;
int i;
puts ("<html>");
puts ("<head>");
html_printGenericStyleSheet (12);
puts ("<title>geneFusions Details</title>\n");
puts ("</head>");
puts ("<body>");
buffer = stringCreate (100);
stringPrintf (buffer, "%s/%s.gfr", confp_get(Conf, "WEB_DATA_DIR"),argv[1]);
gfr_init (string (buffer));
while (currGE = gfr_nextEntry ()){
fflush( stdout );
if (!strEqual (currGE->id,argv[2])) {
continue;
}
printf ("<h1>Detailed summary for potential gene fusion candidate</h1><br>");
puts ("<table border=0 cellpadding=10>");
puts ("<tr align=left valign=top>");
puts ("<td width=400>");
puts ("<h2>Summary information</h2><br>");
printf ("<b>Identifier</b>: %s<br><br>\n",currGE->id);
printf ("<b>Number of inter paired-end reads</b>: %d<br><br>\n",currGE->numInter);
printf ("<b>Type</b>: %s<br><br>\n",currGE->fusionType);
stringPrintf(buffer, "%s/GFF/%s.gff", confp_get(Conf, "WEB_DATA_DIR"),currGE->id);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
if (ftmp) {
printf("<b>Connected Reads</b>: <a href=%s&hgt.customText=%s/GFF/%s.gff target=blank>UCSC connectivity graph</a><br>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),currGE->id);
fclose( ftmp );
}
puts ("</td>");
puts ("<td>");
puts ("<h2>Transcript connectivity graph</h2>");
printf ("<img src=%s/IMAGES/%s.jpg alt=geneFusionImage>\n", confp_get(Conf, "WEB_DATA_LINK"), currGE->id);
puts ("</td>");
puts ("<td>");
puts ("<h2>Transcript connectivity table</h2><br>");
puts ("<table border=0>");
puts ("<tr align=left>");
puts ("<th width=200>Pair Type</th>");
puts ("<th width=200>Entry transcript 1</th>");
puts ("<th width=200>Entry transcript 2</th>");
puts ("<th width=200>Counts</th>");
puts ("</tr>");
fflush( stdout );
for (i = 0; i < arrayMax (currGE->pairCounts); i++) {
currGEPC = arrp (currGE->pairCounts,i,GfrPairCount);
printf ("<tr><td>%s</td><td>%s</td><td>%s</td><td>%.2f</td></tr>\n",
getPairTypeName(currGEPC->pairType),
getEntryNumber(currGEPC->number1, currGEPC->pairType, 1),
getEntryNumber(currGEPC->number2, currGEPC->pairType, 2),
currGEPC->count);
}
puts ("</table>");
puts ("</td>");
puts ("</tr>");
puts ("</table>");
puts ("<br>");
puts ("<h2>Transcript information</h2><br>");
puts ("<table border=1 cellpadding=10 width=\"80%\">");
puts ("<tr align=left>");
puts ("<th width=\"20%\"></th>");
puts ("<th><font color='blue'>Transcript 1</font></th>");
puts ("<th><font color='orange'>Transcript 2</font></th>");
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Gene symbol(s)</b></td>");
printf ("<td width=\"30%%\"><font color='blue'>%s</font></td>\n",processString (currGE->geneSymbolTranscript1));
printf ("<td width=\"30%%\"><font color='orange'>%s</font></td>\n",processString (currGE->geneSymbolTranscript2));
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Coordinates</b></td>");
printf ("<td width=\"30%%\">%s:%d-%d</td>\n",currGE->chromosomeTranscript1,currGE->startTranscript1,currGE->endTranscript1);
printf ("<td width=\"30%%\">%s:%d-%d</td>\n",currGE->chromosomeTranscript2,currGE->startTranscript2,currGE->endTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Strand</b></td>");
printf ("<td width=\"30%%\">%c</td>\n",currGE->strandTranscript1);
printf ("<td width=\"30%%\">%c</td>\n",currGE->strandTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Gene description(s)</b></td>");
printf ("<td width=\"30%%\">%s</td>\n",processString (currGE->descriptionTranscript1));
printf ("<td width=\"30%%\">%s</td>\n",processString (currGE->descriptionTranscript2));
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Number of exons</b></td>");
printf ("<td width=\"30%%\">%d</td>\n",currGE->numExonsTranscript1);
printf ("<td width=\"30%%\">%d</td>\n",currGE->numExonsTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Number of intra paired-end reads</b></td>");
printf ("<td width=\"30%%\">%d</td>\n",currGE->numIntra1);
printf ("<td width=\"30%%\">%d</td>\n",currGE->numIntra2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Links</b></td>");
printf ("<td width=\"30%%\">[<a href=%s&hgt.customText=%s/BED/%s_1.bed target=blank>UCSC genome browser</a>] [<a href=%s/FASTA/%s_1.fasta>FASTA file</a>]<br></td>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td width=\"30%%\">[<a href=%s&hgt.customText=%s/BED/%s_2.bed target=blank>UCSC genome browser</a>] [<a href=%s/FASTA/%s_2.fasta>FASTA file</a>]<br></td></tr>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Expression</b></td>");
stringPrintf(buffer, "%s/BGRS/%s_%s.bgr.gz",
confp_get(Conf, "WEB_DATA_DIR"),
argv[1],
currGE->chromosomeTranscript1);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
puts("<td width=\"30%\">");
if( ftmp ) {
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target=blank>Expression %s</a>]",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
argv[1],
currGE->chromosomeTranscript1,
currGE->chromosomeTranscript1);
fclose(ftmp);
}
puts("</td>");
stringPrintf(buffer, "%s/BGRS/%s_%s.bgr.gz", confp_get(Conf, "WEB_DATA_DIR"),argv[1],currGE->chromosomeTranscript2);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
puts("<td width=\"30%\">");
if( ftmp ) {
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target=blank>Expression %s</a>]",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
argv[1],
currGE->chromosomeTranscript2,
currGE->chromosomeTranscript2);
fclose(ftmp);
}
puts("</td>");
puts("</tr>");
puts ("</table><br><br>");
puts ("<h2>Breakpoint analysis</h2><br>");
puts ("<table border=1 width=\"80%\" cellpadding=10><thead><tr><th>Orientation</th><th>Alignments</th><th colspan=2>Breakpoints</th></tr></thead><tbody>");
puts ("<tr><td>Orientation AB</td>");
if (currGE->strandTranscript1=='+') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "AB_trans1F_trans2F") : stringPrintf(buffer, "AB_trans1F_trans2R");
} else if( currGE->strandTranscript1 == '-') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "AB_trans1R_trans2F") : stringPrintf(buffer, "AB_trans1R_trans2R");
} else {
die("Strand informatation is not correct (transcript 1): %c", currGE->strandTranscript1);
}
printf ("<td align=center><a href=%s/ALIGNMENTS/%s_AB_breakPointAlignments.txt><img src=%s/IMAGES/%s.png></img> AB</a></td>",
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
string(buffer));
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_AB_breakPointsTranscript1.wig target=blank>Breakpoints transcript 1 UCSC Genome Browser</a></td>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_AB_breakPointsTranscript2.wig target=blank>Breakpoints transcript 2 UCSC Genome Browser</a></td></tr>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
fflush(stdout);
puts ("<tr><td>Orientation BA</td>");
if (currGE->strandTranscript1 == '+') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "BA_trans1F_trans2F") : stringPrintf(buffer, "BA_trans1F_trans2R");
} else if( currGE->strandTranscript1 == '-') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "BA_trans1R_trans2F") : stringPrintf(buffer, "BA_trans1R_trans2R");
} else {
die("Strand informatation is not correct (transcript2): %c", currGE->strandTranscript2);
}
printf ("<td align=center><a href=%s/ALIGNMENTS/%s_BA_breakPointAlignments.txt><img src=%s/IMAGES/%s.png></img> BA</a></td>",
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
string(buffer));
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_BA_breakPointsTranscript2.wig target=blank>Breakpoints transcript 2 UCSC Genome Browser</a></td>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_BA_breakPointsTranscript1.wig target=blank>Breakpoints transcript 1 UCSC Genome Browser</a></td></tr>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
puts ("</tbody></table>");
puts ("<br><br><br>");
fflush(stdout);
puts ("<h2>Read coordinates</h2><br>");
puts ("<table border=0>");
puts ("<tr align=left>");
puts ("<th width=\"10%\">Pair Type</th>");
puts ("<th width=\"10%\">Entry Transcript 1</th>");
puts ("<th width=\"10%\">Read start transcript 1</th>");
puts ("<th width=\"10%\">Read end transcript 1</th>");
puts ("<th width=\"10%\">Entry Transcript 2</th>");
puts ("<th width=\"10%\">Read start transcript 2</th>");
puts ("<th width=\"10%\">Read end transcript 2</th>");
puts ("</tr>");
for (i = 0; i < arrayMax (currGE->interReads); i++) {
currGIR = arrp (currGE->interReads,i,GfrInterRead);
printf ("<tr><td>%s</td><td>%s</td><td>%d</td><td>%d</td><td>%s</td><td>%d</td><td>%d</td></tr>\n",
getPairTypeName(currGIR->pairType),
getEntryNumber(currGIR->number1, currGIR->pairType, 1),
currGIR->readStart1,currGIR->readEnd1,
getEntryNumber(currGIR->number2,currGIR->pairType, 2),
currGIR->readStart2,
currGIR->readEnd2);
}
puts ("</table><br><br><br>");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
}
confp_close(Conf);
return EXIT_SUCCESS;
}
int main (int argc, char *argv[])
{
char *queryString;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL)
return EXIT_FAILURE;
cgiInit();
cgiHeader("text/html");
queryString = cgiGet2Post();
if (queryString[0] == '\0') {
puts ("<html>");
puts ("<head>");
html_printGenericStyleSheet (12);
puts ("<title>geneFusions</title>\n");
puts ("</head>");
puts ("<body>");
puts ("<h1>Identification of potential gene fusions using paired-end reads</h1><br><br>");
printf ("<form action=%s/geneFusions_cgi method=get>", confp_get(Conf, "WEB_URL_CGI"));
puts ("<b>Data prefix</b>: ");
puts ("<input type=text name=prefix>");
puts ("<br><br><br>");
puts ("<b>Minimum number of paired-end reads connecting two genes</b>: ");
puts ("<select name=minNum>");
puts ("<option value=2>2");
puts ("<option value=3>3");
puts ("<option value=5 selected>5");
puts ("<option value=10>10");
puts ("</select>");
puts ("<br><br><br>");
puts ("<b>Type of gene fusion</b>: ");
puts ("<select name=type>");
puts ("<option value=read-through>Read-through events");
puts ("<option value=cis>Cis events");
puts ("<option value=intra>Intra-chromosomal events");
puts ("<option value=same>Genes on the same chromosome");
puts ("<option value=inter>Genes on different chromosomes");
puts ("<option value=all selected>All potential gene fusions");
puts ("</select>");
puts ("<br><br><br>");
puts ("<input type=submit value=Submit>");
puts ("<input type=reset value=Reset>");
puts ("</form>");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
else {
int first;
Stringa item = stringCreate (20);
Stringa value = stringCreate (20);
char *iPtr,*vPtr,*prefix,*type;
int minNum;
first = 1;
cgiGetInit ();
while (cgiGetNextPair (&first,item,value)) {
iPtr = string (item);
vPtr = string (value);
if (strEqual (iPtr,"prefix")) {
prefix = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"type")) {
type = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"minNum")) {
minNum = atoi (vPtr);
}
}
generateOutput (prefix,type,minNum);
}
confp_close(Conf);
return EXIT_SUCCESS;
}
SEXP r_cgiHeader(SEXP header) {
char *fn=cStr(header);
cgiHeader(fn);
return R_NilValue;
}
