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sync with tag changes in miniprot

This commit is contained in:
Heng Li 2022-09-09 14:48:17 -04:00
parent 843729df1e
commit 6252e5e367
1 changed files with 19 additions and 8 deletions
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27
misc/paftools.js
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@ -3164,22 +3164,27 @@ function paf_paf2gff(args) {
var hid = 1, last_name = null;
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0] != last_name) last_name = t[0], hid = 1;
else ++hid;
for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
for (var i = 6; i <= 11; ++i) t[i] = parseInt(t[i]);
var cigar = null, score = null, np = null, ds = null;
var cigar = null, score = null, np = null, dist_stop = null, dist_start = null;
for (var i = 12; i < t.length; ++i) {
if ((m = /^(cg:Z|AS:i|np:i|ds:i):(\S+)/.exec(t[i])) != null) {
if ((m = /^(cg:Z|AS:i|np:i|da:i|do:i):(\S+)/.exec(t[i])) != null) {
if (m[1] == 'cg:Z') cigar = m[2];
else if (m[1] == 'AS:i') score = parseInt(m[2]);
else if (m[1] == 'np:i') np = parseInt(m[2]);
else if (m[1] == 'ds:i') ds = parseInt(m[2]);
else if (m[1] == 'do:i') dist_stop = parseInt(m[2]);
else if (m[1] == 'da:i') dist_start = parseInt(m[2]);
}
}
if (cigar == null) throw Error("failed to find the cg:Z tag");
if (score == null) throw Error("failed to find the AS:i tag");
var st = 0, en = 0, phase = 0, pseudo = false, fs = 0, a = [];
if (dist_start != null && dist_start == 0)
a.push([t[5], 'paf2gff', 'start_codon', 0, 3, 0, t[4], '.', 0]);
while ((m = re_cigar.exec(cigar)) != null) {
var len = parseInt(m[1]);
if (m[2] == 'M' || m[2] == 'D') {
@ -3199,16 +3204,22 @@ function paf_paf2gff(args) {
}
a.push([t[5], 'paf2gff', 'exon', st, en, 0, t[4], phase, fs]);
if (en != t[8] - t[7]) throw Error("inconsistent cigar");
if (ds != null && ds == 0)
if (dist_stop != null && dist_stop == 0)
a.push([t[5], 'paf2gff', 'stop_codon', en, en + 3, 0, t[4], '.', 0]);
var type = pseudo? 'pseudogene' : 'protein_coding';
var attr = ['transcript_id=' + t[0] + '#' + hid, 'transcript_type=' + type].join(";");
var trans_attr = 'identity=' + (t[9] / t[10]).toFixed(4);
if (np != null) trans_attr += ';positive=' + (np * 3 / t[10]).toFixed(4);
trans_attr += ';dist_start=' + t[2];
trans_attr += ';dist_end=' + (t[1] - t[3]);
if (ds != null && ds >= 0) trans_attr += ';dist_stop_codon=' + ds;
print([t[5], 'paf2gff', 'transcript', t[7] + 1, t[8], score, t[4], '.', attr + ';' + trans_attr].join("\t"));
trans_attr += ';aa_start=' + t[2];
trans_attr += ';aa_end=' + (t[1] - t[3]);
if (dist_start != null && dist_start >= 0) trans_attr += ';dist_start_codon=' + dist_start;
if (dist_stop != null && dist_stop >= 0) trans_attr += ';dist_stop_codon=' + dist_stop;
var trans_st = t[7], trans_en = t[8];
if (dist_stop != null && dist_stop == 0) {
if (t[4] == '-') trans_st -= 3;
else trans_en += 3;
}
print([t[5], 'paf2gff', 'transcript', trans_st + 1, trans_en, score, t[4], '.', attr + ';' + trans_attr].join("\t"));
if (opt.aa && t[4] == '-') {
var b = [], len = t[8] - t[7];
for (var i = a.length - 1; i >= 0; --i) {