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);
}
/**
* Initialize the FASTQ module using a pipe.
* @post fastq_nextSequence(), fastq_readAllSequences() can be called.
*/
void fastq_initFromPipe (char* command)
{
lsFastq = ls_createFromPipe (command);
ls_bufferSet (lsFastq,1);
}
/**
* Initialize the blastParser module from pipe.
* @param[in] command Command to be executed
*/
void blastParser_initFromPipe (char* command)
{
ls = ls_createFromPipe (command);
ls_bufferSet (ls,1);
}
