63 lines
1.6 KiB
JavaScript
63 lines
1.6 KiB
JavaScript
|
var min_ovlp = 30;
|
||
|
|
|
||
|
|
if (arguments.length < 3) {
|
||
|
|
print("Usage: k8 selctg.js <HLA-gene> <HLA-ALT-exons.bed> <ctg-to-ALT.sam> [min_ovlp="+min_ovlp+"]");
|
||
|
|
exit(1);
|
||
|
|
}
|
||
|
|
|
||
|
|
if (arguments.length >= 4) min_ovlp = parseInt(arguments[3]);
|
||
|
|
var gene = arguments[0];
|
||
|
|
|
||
|
|
var buf = new Bytes();
|
||
|
|
|
||
|
|
var h = {};
|
||
|
|
var file = new File(arguments[1]);
|
||
|
|
while (file.readline(buf) >= 0) {
|
||
|
|
var t = buf.toString().split("\t");
|
||
|
|
if (t[3] != gene) continue;
|
||
|
|
if (h[t[0]] == null) h[t[0]] = [];
|
||
|
|
h[t[0]].push([parseInt(t[1]), parseInt(t[2])]);
|
||
|
|
}
|
||
|
|
file.close();
|
||
|
|
|
||
|
|
var s = {}, re = /(\d+)([MIDSHN])/g;
|
||
|
|
file = new File(arguments[2]);
|
||
|
|
while (file.readline(buf) >= 0) {
|
||
|
|
var line = buf.toString();
|
||
|
|
var m, t = line.split("\t");
|
||
|
|
var x = h[t[2]];
|
||
|
|
if (x == null) continue;
|
||
|
|
|
||
|
|
var start = parseInt(t[3]) - 1, end = start;
|
||
|
|
while ((m = re.exec(t[5])) != null) // parse CIGAR to get the end position
|
||
|
|
if (m[2] == 'M' || m[2] == 'D')
|
||
|
|
end += parseInt(m[1]);
|
||
|
|
|
||
|
|
var max_ovlp = 0;
|
||
|
|
for (var i = 0; i < x.length; ++i) {
|
||
|
|
var max_left = x[i][0] > start? x[i][0] : start;
|
||
|
|
var min_rght = x[i][1] < end ? x[i][1] : end;
|
||
|
|
max_ovlp = max_ovlp > min_rght - max_left? max_ovlp : min_rght - max_left;
|
||
|
|
}
|
||
|
|
|
||
|
|
var AS = null, XS = null;
|
||
|
|
if ((m = /AS:i:(\d+)/.exec(line)) != null) AS = parseInt(m[1]);
|
||
|
|
if ((m = /XS:i:(\d+)/.exec(line)) != null) XS = parseInt(m[1]);
|
||
|
|
|
||
|
|
if (s[t[0]] == null) s[t[0]] = [];
|
||
|
|
s[t[0]].push([AS, XS, max_ovlp]);
|
||
|
|
}
|
||
|
|
file.close();
|
||
|
|
|
||
|
|
buf.destroy();
|
||
|
|
|
||
|
|
for (var x in s) {
|
||
|
|
var is_rejected = false, y = s[x];
|
||
|
|
y.sort(function(a,b) {return b[0]-a[0]});
|
||
|
|
for (var i = 0; i < y.length && y[i][0] == y[0][0]; ++i)
|
||
|
|
if (y[0][2] < min_ovlp || y[i][0] == y[i][1])
|
||
|
|
is_rejected = true;
|
||
|
|
if (is_rejected) continue;
|
||
|
|
print(x);
|
||
|
|
}
|