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convert PAF to LAST's cigar output 

also added the support of BLAST-like output for "--cs=short".
This commit is contained in:
Heng Li 2017-11-17 09:42:16 -05:00
parent 662d05dc02
commit 39a9666246
1 changed files with 64 additions and 39 deletions
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103
misc/paf2aln.js
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@ -36,20 +36,21 @@ var getopt = function(args, ostr) {
return optopt;
}
var c, maf_out = false, line_len = 80;
while ((c = getopt(arguments, "ml:")) != null) {
if (c == 'm') maf_out = true;
else if (c == 'l') line_len = parseInt(getopt.arg); // TODO: not implemented yet
var c, line_len = 80, fmt = "aln";
while ((c = getopt(arguments, "f:l:")) != null) {
if (c == 'f') {
fmt = getopt.arg;
if (fmt != "aln" && fmt != "lastz-cigar" && fmt != "maf")
throw Error("format must be one of aln, lastz-cigar and maf");
} else if (c == 'l') line_len = parseInt(getopt.arg);
}
if (line_len == 0) line_len = 0x7fffffff;
if (getopt.ind == arguments.length) {
print("Usage: k8 paf2aln.js [options] <with-cs.paf>");
print("Usage: k8 paf2aln.js [options] <in.paf>");
print("Options:");
print(" -m MAF output (BLAST-like output by default)");
print(" -f STR output format: aln (BLAST-like), maf or lastz-cigar [aln]");
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);
}
@ -66,7 +67,7 @@ function padding_str(x, len, right)
function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
{
var l = type == '*'? 1 : seq.length;
if (type == '=') {
if (type == '=' || type == ':') {
s_ref.set(seq);
s_qry.set(seq);
s_mid.set(Array(l+1).join("|"));
@ -96,49 +97,73 @@ function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
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(" "));
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 re = /([=\-\+\*])([A-Za-z]+)/g;
var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes(); // these are used to show padded alignment
var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
var re_cg = /(\d+)([MIDNSH])/g;
var buf = new Bytes();
var file = new File(arguments[getopt.ind]);
if (maf_out) print("##maf version=1\n");
var file = arguments[getopt.ind] == "-"? new File() : new File(arguments[getopt.ind]);
var lineno = 0;
if (fmt == "maf") print("##maf version=1\n");
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
var t = line.split("\t", 12);
if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue;
var cs = m[1];
++lineno;
s_ref.length = s_qry.length = s_mid.length = 0;
var slen = [0, 0], elen = [0, 0];
if (maf_out) {
while ((m = re.exec(cs)) != null)
update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
if (maf_out) {
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;
print("a " + score);
print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
var qs, qe, ql = parseInt(t[1]);
if (t[4] == '+') {
qs = parseInt(t[2]);
qe = parseInt(t[3]);
} else {
qs = ql - parseInt(t[3]);
qe = ql - parseInt(t[2]);
}
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(" "));
print("");
if (fmt == "lastz-cigar") { // LASTZ-cigar output
var cg = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
if (cg == null) {
warn("WARNING: converting to LASTZ-cigar format requires the 'cg' tag, which is absent on line " + lineno);
continue;
}
} else {
line = line.replace(/\tc[sg]:Z:\S+/g, "");
var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? m[1] : 0;
var out = ['cigar:', t[0], t[2], t[3], t[4], t[5], t[7], t[8], '+', score];
while ((m = re_cg.exec(cg)) != null)
out.push(m[2], m[1]);
print(out.join(" "));
} else if (fmt == "maf") { // MAF output
var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
if (cs == null) {
warn("WARNING: converting to MAF requires the 'cs' tag, which is absent on line " + lineno);
continue;
}
while ((m = re_cs.exec(cs)) != null) {
if (m[1] == ':')
throw Error("converting to MAF only works with 'minimap2 --cs=long'");
update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
}
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;
print("a " + score);
print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
var qs, qe, ql = parseInt(t[1]);
if (t[4] == '+') {
qs = parseInt(t[2]);
qe = parseInt(t[3]);
} else {
qs = ql - parseInt(t[3]);
qe = ql - parseInt(t[2]);
}
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(" "));
print("");
} else { // BLAST-like output
var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
if (cs == null) {
warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
continue;
}
line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
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) {
while ((m = re_cs.exec(cs)) != null) {
if (m[1] == ':') m[2] = Array(parseInt(m[2]) + 1).join("=");
var start = 0, rest = m[1] == '*'? 1 : m[2].length;
while (rest > 0) {
var l_proc;