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blast-like output working

This commit is contained in:
Heng Li 2017-08-04 14:31:21 -04:00
parent 71f82759af
commit fd66ab5413
1 changed files with 77 additions and 31 deletions
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108
misc/paf2aln.js
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@ -36,14 +36,20 @@ var getopt = function(args, ostr) {
return optopt; return optopt;
} }
var c, maf_out = false, line_len = 0; var c, maf_out = false, line_len = 80;
while ((c = getopt(arguments, "ml:")) != null) { while ((c = getopt(arguments, "ml:")) != null) {
if (c == 'm') maf_out = true; if (c == 'm') maf_out = true;
else if (c == 'l') line_len = parseInt(getopt.arg); // TODO: not implemented yet else if (c == 'l') line_len = parseInt(getopt.arg); // TODO: not implemented yet
} }
if (line_len == 0) line_len = 0x7fffffff;
if (getopt.ind == arguments.length) { if (getopt.ind == arguments.length) {
print("Usage: k8 paf2aln.js [options] <with-cs.paf>"); print("Usage: k8 paf2aln.js [options] <with-cs.paf>");
print("Options:");
print(" -m MAF output (BLAST-like output by default)");
print(" -l INT line length in BLAST-like output [80]");
print("");
print("Note: this script only works when minimap2 is run with option '-S'");
exit(1); exit(1);
} }
@ -57,6 +63,42 @@ function padding_str(x, len, right)
return s; return s;
} }
function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
{
var l = type == '*'? 1 : seq.length;
if (type == '=') {
s_ref.set(seq);
s_qry.set(seq);
s_mid.set(Array(l+1).join("|"));
slen[0] += l, slen[1] += l;
} else if (type == '*') {
s_ref.set(seq.charAt(0));
s_qry.set(seq.charAt(1));
s_mid.set(' ');
slen[0] += 1, slen[1] += 1;
} else if (type == '+') {
s_ref.set(Array(l+1).join("-"));
s_qry.set(seq);
s_mid.set(Array(l+1).join(" "));
slen[1] += l;
} else if (type == '-') {
s_ref.set(seq);
s_qry.set(Array(l+1).join("-"));
s_mid.set(Array(l+1).join(" "));
slen[0] += l;
}
}
function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
{
print(["Ref+:", padding_str(rs + slen[0] + 1, 10, false), s_ref.toString(), padding_str(rs + elen[0], 10, true)].join(" "));
print(" " + s_mid.toString());
var st, en;
if (strand == '+') st = qs + slen[1] + 1, en = qs + elen[1];
else st = qs - slen[1], en = qs - elen[1] + 1;
print(["Qry" + strand + ":", padding_str(st, 10, false), s_qry.toString(), padding_str(en , 10, true)].join(" "));
}
var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes(); var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes();
var re = /([=\-\+\*])([A-Za-z]+)/g; var re = /([=\-\+\*])([A-Za-z]+)/g;
@ -69,32 +111,10 @@ while (file.readline(buf) >= 0) {
if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue; if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue;
var cs = m[1]; var cs = m[1];
s_ref.length = s_qry.length = s_mid.length = 0; s_ref.length = s_qry.length = s_mid.length = 0;
if (line_len == 0 || maf_out) { var slen = [0, 0], elen = [0, 0];
var ql = 0, tl = 0, al = 0; if (maf_out) {
var n_mm = 0, n_gap = 0; while ((m = re.exec(cs)) != null)
while ((m = re.exec(cs)) != null) { update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
var l = m[2].length;
if (m[1] == '=') {
s_ref.set(m[2]);
s_qry.set(m[2]);
s_mid.set(Array(l+1).join("|"));
} else if (m[1] == '*') {
s_ref.set(m[2].charAt(0));
s_qry.set(m[2].charAt(1));
s_mid.set(' ');
++n_mm;
} else if (m[1] == '+') {
s_ref.set(Array(l+1).join("-"));
s_qry.set(m[2]);
s_mid.set(Array(l+1).join(" "));
n_gap += l;
} else if (m[1] == '-') {
s_ref.set(m[2]);
s_qry.set(Array(l+1).join("-"));
s_mid.set(Array(l+1).join(" "));
n_gap += l;
}
}
if (maf_out) { if (maf_out) {
var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0; var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
var len = t[0].length > t[5].length? t[0].length : t[5].length; var len = t[0].length > t[5].length? t[0].length : t[5].length;
@ -112,11 +132,37 @@ while (file.readline(buf) >= 0) {
print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false), print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false),
t[4], padding_str(ql, 10, false), s_qry.toString()].join(" ")); t[4], padding_str(ql, 10, false), s_qry.toString()].join(" "));
print(""); print("");
} else {
print(line);
print(n_mm, n_gap);
print(s_ref); print(s_mid); print(s_qry);
} }
} else {
line = line.replace(/\tc[sg]:Z:\S+/g, "");
print('>' + line);
var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
var n_blocks = 0;
while ((m = re.exec(cs)) != null) {
var start = 0, rest = m[1] == '*'? 1 : m[2].length;
while (rest > 0) {
var l_proc;
if (s_ref.length + rest >= line_len) {
l_proc = line_len - s_ref.length;
update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
if (n_blocks > 0) print("");
print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
++n_blocks;
s_ref.length = s_qry.length = s_mid.length = 0;
slen[0] = elen[0], slen[1] = elen[1];
} else {
l_proc = rest;
update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
}
rest -= l_proc, start += l_proc;
}
}
if (s_ref.length > 0) {
if (n_blocks > 0) print("");
print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
++n_blocks;
}
print("//");
} }
} }
file.close(); file.close();