static void xml_outputAGSline(const GthAGS *ags, unsigned long agsnum,
unsigned int indentlevel, GtFile *outfp)
{
GthExonAGS *exon;
unsigned long i;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<AGS_line AGS_serial=\"%lu\">\n",
agsnum + OUTPUTOFFSET);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon_coordinates>\n");
indentlevel++;
for (i = 0; i < gth_ags_num_of_exons(ags); i++) {
exon = gth_ags_get_exon(ags, i);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_start=\"%lu\" e_stop=\"%lu\"/>\n",
SHOWGENPOSAGS(exon->range.start),
SHOWGENPOSAGS(exon->range.end));
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon_coordinates>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</AGS_line>\n");
}
static void outputAGSline(const GthAGS *ags, GtUword agsnum,
GtFile *outfp)
{
GthExonAGS *exon;
GtUword i;
gt_file_xprintf(outfp, "AGS-" GT_WU " (", agsnum + OUTPUTOFFSET);
for (i = 0; i < gth_ags_num_of_exons(ags); i++) {
exon = gth_ags_get_exon(ags, i);
if (i > 0)
gt_file_xfputc(',', outfp);
gt_file_xprintf(outfp, GT_WU " " GT_WU, SHOWGENPOSAGS(exon->range.start),
SHOWGENPOSAGS(exon->range.end));
}
gt_file_xprintf(outfp, ")\n");
}
static void output_exon_intron_lines(const GthAGS *ags, int widthforgenpos,
GtFile *outfp)
{
GthSpliceSiteProb *splicesiteprob;
GthExonAGS *exon;
GtUword i, leftexonborder, rightexonborder, exonlength,
leftintronborder = GT_UNDEF_UWORD, rightintronborder,
intronlength;
GthDbl exonscore;
GthFlt donorsiteprob, acceptorsiteprob;
for (i = 0; i < gt_array_size(ags->exons); i++) {
exon = (GthExonAGS*) gt_array_get(ags->exons, i);
leftexonborder = exon->range.start;
rightexonborder = exon->range.end;
exonlength = rightexonborder - leftexonborder + 1;
exonscore = exon->score;
if (i > 0) {
rightintronborder = leftexonborder - 1;
intronlength = rightintronborder - leftintronborder + 1;
splicesiteprob = (GthSpliceSiteProb*)
gt_array_get(ags->splicesiteprobs, i-1);
donorsiteprob = splicesiteprob->donorsiteprob;
acceptorsiteprob = splicesiteprob->acceptorsiteprob;
/* output intron */
gt_file_xprintf(outfp,
" Intron %2" GT_WUS " %*" GT_WUS " %*" GT_WUS " (%4"
GT_WUS " n); " "Pd: %5.3f Pa: %5.3f\n",
i - 1 + OUTPUTOFFSET, widthforgenpos,
SHOWGENPOSAGS(leftintronborder), widthforgenpos,
SHOWGENPOSAGS(rightintronborder), intronlength,
donorsiteprob, acceptorsiteprob);
}
leftintronborder = rightexonborder + 1;
/* output exon */
gt_file_xprintf(outfp,
" Exon %2" GT_WUS " %*" GT_WUS " %*" GT_WUS " (%4" GT_WUS
" n); score: %5.3f\n",
i + OUTPUTOFFSET, widthforgenpos,
SHOWGENPOSAGS(leftexonborder), widthforgenpos,
SHOWGENPOSAGS(rightexonborder), exonlength, exonscore);
}
gt_file_xfputc('\n', outfp);
}
static void xml_output_exon_intron_lines(const GthAGS *ags,
unsigned int indentlevel,
GtFile *outfp)
{
GthSpliceSiteProb *splicesiteprob;
GthExonAGS *exon;
unsigned long i, leftexonborder, rightexonborder, exonlength,
leftintronborder = GT_UNDEF_ULONG, rightintronborder,
intronlength;
GthDbl exonscore;
GthFlt donorsiteprob, acceptorsiteprob;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<exon-intron_info xmlns=\"http://www.genomethreader.org/"
"GTH_output/PGL_module/predicted_gene_location/"
"AGS_information/exon-intron_info/\">\n");
indentlevel++;
for (i = 0; i < gt_array_size(ags->exons); i++) {
exon = (GthExonAGS*) gt_array_get(ags->exons, i);
leftexonborder = exon->range.start;
rightexonborder = exon->range.end;
exonlength = rightexonborder - leftexonborder + 1;
exonscore = exon->score;
if (i > 0) {
rightintronborder = leftexonborder - 1;
intronlength = rightintronborder - leftintronborder + 1;
splicesiteprob = (GthSpliceSiteProb*)
gt_array_get(ags->splicesiteprobs, i-1);
donorsiteprob = splicesiteprob->donorsiteprob;
acceptorsiteprob = splicesiteprob->acceptorsiteprob;
/* output intron */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<intron i_serial=\"%lu\" don_prob=\"%.3f\" "
"acc_prob=\"%.3f\">\n", i - 1 + OUTPUTOFFSET,
donorsiteprob, acceptorsiteprob);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<gDNA_intron_boundary i_start=\"%lu\" i_stop=\"%lu\" "
"i_length=\"%lu\"/>\n",
SHOWGENPOSAGS(leftintronborder),
SHOWGENPOSAGS(rightintronborder), intronlength);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</intron>\n");
}
leftintronborder = rightexonborder + 1;
/* output exon */
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<exon e_serial=\"%lu\" e_score=\"%.3f\">\n",
i + OUTPUTOFFSET, exonscore);
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp,
"<gDNA_exon_boundary e_start=\"%lu\" e_stop=\"%lu\" "
"e_length=\"%lu\"/>\n", SHOWGENPOSAGS(leftexonborder),
SHOWGENPOSAGS(rightexonborder), exonlength);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon>\n");
}
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</exon-intron_info>\n");
}
