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r981: asmgene to check duplicate genes

This commit is contained in:
Heng Li 2020-04-14 15:52:36 -04:00
parent 50775362bb
commit f10dff78dc
1 changed files with 17 additions and 5 deletions
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22
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.17-r980-dirty';
var paftools_version = '2.17-r981-dirty';
/*****************************
***** Library functions *****
@ -905,14 +905,14 @@ function paf_asmgene(args)
gene_nr[gene_list[last][0]] = 1;
// count and print
var col1 = ["full_sgl", "full_dup", "frag", "part50+", "part10+", "part10-"];
var col1 = ["full_sgl", "full_dup", "frag", "part50+", "part10+", "part10-", "dup_cnt", "dup_sum"];
var rst = [];
for (var k = 0; k < col1.length; ++k) {
rst[k] = [];
for (var i = 0; i < n_fn; ++i)
rst[k][i] = 0;
}
for (var g in gene) {
for (var g in gene) { // count single-copy genes
if (gene[g][0] == null || gene[g][0][0] != 1) continue;
if (gene_nr[g] == null) continue;
if (auto_only && /^(chr)?[XY]$/.test(refpos[g][2])) continue;
@ -920,8 +920,9 @@ function paf_asmgene(args)
if (gene[g][i] == null) {
rst[5][i]++;
if (print_err) print('M', header[i], refpos[g].join("\t"));
} else if (gene[g][i][0] == 1) rst[0][i]++;
else if (gene[g][i][0] > 1) {
} else if (gene[g][i][0] == 1) {
rst[0][i]++;
} else if (gene[g][i][0] > 1) {
rst[1][i]++;
if (print_err) print('D', header[i], refpos[g].join("\t"));
} else if (gene[g][i][1] >= opt.min_cov) {
@ -939,6 +940,17 @@ function paf_asmgene(args)
}
}
}
for (var g in gene) { // count multi-copy genes
if (gene[g][0] == null || gene[g][0][0] == 1) continue;
if (gene_nr[g] == null) continue;
if (auto_only && /^(chr)?[XY]$/.test(refpos[g][2])) continue;
for (var i = 0; i < n_fn; ++i) {
if (gene[g][i] != null && gene[g][i][0] > 1) {
rst[6][i]++;
rst[7][i] += gene[g][i][0];
}
}
}
print('H', 'Metric', header.join("\t"));
for (var k = 0; k < rst.length; ++k) {
print('X', col1[k], rst[k].join("\t"));