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This commit is contained in:
Heng Li 2022-09-08 23:18:13 -04:00
parent e450f161bb
commit a2e6659d9b
1 changed files with 8 additions and 3 deletions
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11
misc/paftools.js
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@ -3168,11 +3168,12 @@ function paf_paf2gff(args) {
else ++hid; else ++hid;
for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]); for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
for (var i = 6; i <= 11; ++i) t[i] = parseInt(t[i]); for (var i = 6; i <= 11; ++i) t[i] = parseInt(t[i]);
var cigar = null, score = null; var cigar = null, score = null, np = null;
for (var i = 12; i < t.length; ++i) { for (var i = 12; i < t.length; ++i) {
if ((m = /^(cg:Z|AS:i):(\S+)/.exec(t[i])) != null) { if ((m = /^(cg:Z|AS:i|np:i):(\S+)/.exec(t[i])) != null) {
if (m[1] == 'cg:Z') cigar = m[2]; if (m[1] == 'cg:Z') cigar = m[2];
else if (m[1] == 'AS:i') score = parseInt(m[2]); else if (m[1] == 'AS:i') score = parseInt(m[2]);
else if (m[1] == 'np:i') np = parseInt(m[2]);
} }
} }
if (cigar == null) throw Error("failed to find the cg:Z tag"); if (cigar == null) throw Error("failed to find the cg:Z tag");
@ -3199,7 +3200,11 @@ function paf_paf2gff(args) {
if (en != t[8] - t[7]) throw Error("inconsistent cigar"); if (en != t[8] - t[7]) throw Error("inconsistent cigar");
var type = pseudo? 'pseudogene' : 'protein_coding'; var type = pseudo? 'pseudogene' : 'protein_coding';
var attr = ['transcript_id=' + t[0] + '#' + hid, 'transcript_type=' + type].join(";"); var attr = ['transcript_id=' + t[0] + '#' + hid, 'transcript_type=' + type].join(";");
print([t[5], 'paf2gff', 'transcript', t[7] + 1, t[8], score, t[4], '.', attr].join("\t")); var trans_attr = 'identity=' + (t[9] / t[10]).toFixed(4);
if (np != null) trans_attr += ';positive=' + (np * 3 / t[10]).toFixed(4);
trans_attr += ';find_start=' + (t[2] == 0? 1 : 0);
trans_attr += ';find_end=' + (t[3] == t[1]? 1 : 0);
print([t[5], 'paf2gff', 'transcript', t[7] + 1, t[8], score, t[4], '.', attr + ';' + trans_attr].join("\t"));
if (opt.aa && t[4] == '-') { if (opt.aa && t[4] == '-') {
var b = [], len = t[8] - t[7]; var b = [], len = t[8] - t[7];
for (var i = a.length - 1; i >= 0; --i) { for (var i = a.length - 1; i >= 0; --i) {