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