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option to print all exons for debugging

This commit is contained in:
Heng Li 2017-08-12 10:04:16 -04:00
parent 30b8cb4672
commit 2d11aaa830
1 changed files with 24 additions and 11 deletions
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35
misc/exon-eval.js
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@ -123,12 +123,13 @@ Interval.find_ovlp = function(a, st, en)
* Main function *
*****************/
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_err = false, print_corr = false;
while ((c = getopt(arguments, "l:r:ec")) != null) {
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_ovlp = false, print_err_only = false, first_only = false;
while ((c = getopt(arguments, "l:r:ep1")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg);
else if (c == 'e') print_err = true;
else if (c == 'c') print_corr = true;
else if (c == 'p') print_ovlp = true;
else if (c == 'e') print_err_only = print_ovlp = true;
else if (c == '1') first_only = true;
}
if (arguments.length - getopt.ind < 2) {
@ -162,7 +163,7 @@ 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;
var n_novel = 0, n_partial = 0, n_unmapped = 0, n_mapped = 0, n_exon = 0, n_pri = 0;
var n_ext_hit = 0, n_int_hit = 0, n_sgl_hit = 0;
file = new File(arguments[getopt.ind+1]);
@ -171,11 +172,16 @@ var re_cigar = /(\d+)([MIDNSH])/g;
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0].charAt(0) == '@') continue;
if (last_qname == t[0]) continue;
var flag = parseInt(t[1]);
if (flag&0x100) continue;
if (first_only && last_qname == t[0]) continue;
if (t[2] == '*') {
++n_unmapped;
continue;
} else ++n_mapped;
} else {
++n_pri;
if (last_qname != t[0]) ++n_mapped;
}
var st = parseInt(t[3]) - 1, en = st, exon_st = st;
var exon = [];
while ((m = re_cigar.exec(t[5])) != null) {
@ -225,16 +231,22 @@ while (file.readline(buf) >= 0) {
}
if (hit) break;
}
if ((print_err && !hit) || (print_corr && hit)) {
if (print_ovlp) {
var type = hit? 'C' : 'P';
if (hit && print_err_only) continue;
var x = '[';
for (var j = 0; j < o.length; ++j) {
if (j) x += ', ';
x += '(' + o[j][0] + "," + o[j][1] + ')';
}
x += ']';
print(t[0], i+1, t[2], exon[i][0], exon[i][1], x);
print(type, t[0], i+1, t[2], exon[i][0], exon[i][1], x);
}
} else ++n_novel;
} else {
++n_novel;
if (print_ovlp)
print('N', t[0], i+1, t[2], exon[i][0], exon[i][1]);
}
}
}
last_qname = t[0];
@ -243,9 +255,10 @@ file.close();
buf.destroy();
if (!print_err && !print_corr) {
if (!print_ovlp) {
print("Number of unmapped reads: " + n_unmapped);
print("Number of mapped reads: " + n_mapped);
print("Number of primary alignments: " + n_pri);
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) + "%)");