static void generateOutput (char* prefix, char* typeSelected, int minNum)
{
GfrEntry *currGE;
Stringa buffer;
char *pos;
puts ("<html>");
puts ("<head>");
puts ("<title>Results - Gene Fusions</title>");
html_printGenericStyleSheet (12);
puts ("</head>");
puts ("<body>");
if (prefix[0] == '\0') {
die ("Invalid prefix");
}
printf ("<h1>Results - %s</h1><br><br><br>",prefix);
buffer = stringCreate(50);
//Chromosome expression, if present
LineStream ls;
char* chrSignal=NULL;
stringPrintf(buffer, "ls -1 %s/BGRS/%s_chr*.bgr.gz 2> /dev/null",
confp_get(Conf, "WEB_DATA_DIR"),
prefix);
ls = ls_createFromPipe(string(buffer));
int countCol = 0;
puts ("Expression signal: ");
fflush(stdout);
while( chrSignal = ls_nextLine(ls)) {
char* chrTmp = stringBetween( prefix, ".bgr.gz", chrSignal );
chrTmp++;
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target='blank'>%s</a>] ",
htmlLinker_generateLinkToGenomeBrowserAtUCSC("hg18","vertebrate","human", chrTmp,
confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"),
50000000 + confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
confp_get(Conf, "WEB_DATA_LINK"),
prefix,
chrTmp,
chrTmp);
if (countCol > 10) {
puts( "<BR>" );
countCol=0;
}
countCol++;
}
if( countCol==0) puts( "No data available yet" );
ls_destroy(ls);
puts ("<br><br>");
puts ("For a definition of SPER, DASPER and RESPER see <a href=http://rnaseq.gersteinlab.org/fusionseq/>FusionSeq</a>");
puts ("<br><br>");
puts ("<br><table border=0 width=100% align=center cellpadding=10>");
puts ("<tr align=left>");
puts ("<th>SPER</th>");
puts ("<th>DASPER</th>");
puts ("<th>RESPER</th>");
puts ("<th>Number of inter paired-end reads</th>");
puts ("<th>Type</th>");
puts ("<th>Genomic coordinates</th>");
puts ("<th>Gene symbol</th>");
puts ("<th>Description</th>");
puts ("<th>Genomic coordinates</th>");
puts ("<th>Gene symbol</th>");
puts ("<th>Description</th>");
puts ("<th></th>");
puts ("</tr>");
fflush(stdout);
stringPrintf (buffer,"%s/%s.gfr", confp_get(Conf, "WEB_DATA_DIR"), prefix);
gfr_init (string (buffer));
int countElements = 0;
while (currGE = gfr_nextEntry ()) {
if (currGE->numInter < minNum) {
continue;
}
if (strEqual (typeSelected,"all") || strEqual (currGE->fusionType,typeSelected) ||
( strEqual(currGE->fusionType,"cis") && strEqual( typeSelected,"same") ) ||
( strEqual(currGE->fusionType,"read-through") && strEqual( typeSelected,"same") ) ) {
if (pos = strchr (currGE->descriptionTranscript1,'|')) {
*pos = '\0';
}
if (pos = strchr (currGE->descriptionTranscript2,'|')) {
*pos = '\0';
}
puts ("<tr>");
printf ("<td align=left>%1.3f</td>\n",currGE->SPER);
printf ("<td align=left>%1.3f</td>\n",currGE->DASPER);
printf ("<td align=left>%1.3f</td>\n",currGE->RESPER);
printf ("<td align=left>%d</td>\n",currGE->numInter);
printf ("<td align=left>%s</td>\n",currGE->fusionType);
printf ("<td align=left><a href=%s target=blank>%s:%d-%d</a></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"))),
currGE->chromosomeTranscript1,currGE->startTranscript1,currGE->endTranscript1);
printf ("<td align=left>%s</td>\n",processString (currGE->geneSymbolTranscript1));
printf ("<td align=left>%s</td>\n",currGE->descriptionTranscript1);
printf ("<td align=left><a href=%s target=blank>%s:%d-%d</a></td>\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"))),
currGE->chromosomeTranscript2,currGE->startTranscript2,currGE->endTranscript2);
printf ("<td align=left>%s</td>\n",processString (currGE->geneSymbolTranscript2));
printf ("<td align=left>%s</td>\n",currGE->descriptionTranscript2);
printf ("<td align=left><a href=%s/showDetails_cgi?%s+%s>Details</a></td>\n", confp_get(Conf, "WEB_URL_CGI"), prefix,currGE->id);
puts ("</tr>");
countElements++;
}
}
gfr_deInit ();
stringDestroy (buffer);
puts ("</table><br><br>");
if( countElements == 0) puts("No fusion candidates can be found satisfying all specified criteria.");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
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;
}
