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the final version 

to be replaced by intron-eval
This commit is contained in:
Heng Li 2017-08-20 21:54:35 +08:00
parent 5ed2faf270
commit a4c41f64a5
1 changed files with 19 additions and 6 deletions
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25
misc/exon-eval.js
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@ -123,10 +123,11 @@ Interval.find_ovlp = function(a, st, en)
* Main function *
*****************/
var c, l_fuzzy = 0, min_ov_ratio = 0.95, print_ovlp = false, print_err_only = false, first_only = false;
while ((c = getopt(arguments, "l:r:ep1")) != null) {
var c, l_fuzzy = 0, min_ov_ratio = 0.95, min_span_ratio = 0.9, print_ovlp = false, print_err_only = false, first_only = false;
while ((c = getopt(arguments, "l:r:s:ep1")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg);
else if (c == 's') min_span_ratio = parseFloat(getopt.arg);
else if (c == 'p') print_ovlp = true;
else if (c == 'e') print_err_only = print_ovlp = true;
else if (c == '1') first_only = true;
@ -163,7 +164,7 @@ for (var chr in anno) {
Interval.index_end(e);
}
var n_novel = 0, n_partial = 0, n_unmapped = 0, n_mapped = 0, n_exon = 0, n_pri = 0;
var n_novel = 0, n_int_novel = 0, n_ext_novel = 0, n_sgl_novel = 0, n_partial = 0, n_unmapped = 0, n_mapped = 0, n_exon = 0, n_int_exon = 0, n_pri = 0, n_sgl_exon = 0, n_ext_exon = 0;
var n_ext_hit = 0, n_int_hit = 0, n_sgl_hit = 0;
file = new File(arguments[getopt.ind+1]);
@ -194,9 +195,15 @@ while (file.readline(buf) >= 0) {
}
exon.push([exon_st, en]);
n_exon += exon.length;
n_int_exon += exon.length > 2? exon.length - 2 : 0;
n_sgl_exon += exon.length == 1? 1 : 0;
n_ext_exon += exon.length > 1? 2 : 0;
var chr = anno[t[2]];
if (chr == null) {
n_novel += exon.length;
n_int_novel += exon.length > 2? exon.length - 2 : 0;
n_sgl_novel += exon.length == 1? 1 : 0;
n_ext_novel += exon.length > 1? 2 : 0;
} else {
for (var i = 0; i < exon.length; ++i) {
var o = Interval.find_ovlp(chr, exon[i][0], exon[i][1]);
@ -219,11 +226,11 @@ while (file.readline(buf) >= 0) {
if (i == 0 && exon.length == 1) {
if (ov_ratio >= min_ov_ratio) ++n_sgl_hit, hit = true;
} else if (i == 0) {
if (en_diff <= l_fuzzy) ++n_ext_hit, hit = true;
if (ov_ratio >= min_ov_ratio && en_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else if (i == exon.length - 1) {
if (st_diff <= l_fuzzy) ++n_ext_hit, hit = true;
if (ov_ratio >= min_ov_ratio && st_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else {
if (en_diff + st_diff <= l_fuzzy)
if (en_diff + st_diff <= l_fuzzy && ol / span >= min_span_ratio)
++n_int_hit, hit = true;
}
if (hit) break;
@ -241,6 +248,9 @@ while (file.readline(buf) >= 0) {
}
} else {
++n_novel;
if (i > 0 && i < exon.length - 1) ++n_int_novel;
if (exon.length > 1 && (i == 0 || i == exon.length - 1)) ++n_ext_novel;
if (exon.length == 1) ++n_sgl_novel;
if (print_ovlp)
print('N', t[0], i+1, t[2], exon[i][0], exon[i][1]);
}
@ -259,4 +269,7 @@ if (!print_ovlp) {
print("Number of mapped exons: " + n_exon);
print("Number of novel exons: " + n_novel);
print("Number of correct exons: " + (n_ext_hit + n_int_hit + n_sgl_hit) + " (" + ((n_ext_hit + n_int_hit + n_sgl_hit) / n_exon * 100).toFixed(2) + "%)");
print("Internal exons: " + n_int_novel + ", " + n_int_hit + " / " + n_int_exon + " = " + (n_int_hit / n_int_exon * 100).toFixed(2) + "%");
print("External exons: " + n_ext_novel + ", " + n_ext_hit + " / " + n_ext_exon + " = " + (n_ext_hit / n_ext_exon * 100).toFixed(2) + "%");
print("Singleton exons: " + n_sgl_novel + ", " + n_sgl_hit + " / " + n_sgl_exon + " = " + (n_sgl_hit / n_sgl_exon * 100).toFixed(2) + "%");
}