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added longcs2fa

This commit is contained in:
Heng Li 2022-07-18 22:24:48 -04:00
parent 767556b6f0
commit 15cade0f06
1 changed files with 41 additions and 0 deletions
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41
misc/paftools.js
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@ -3110,6 +3110,45 @@ function paf_pafcmp(args)
buf.destroy(); buf.destroy();
} }
function paf_longcs2seq(args) {
var c, opt = { query:false };
while ((c = getopt(args, "q")) != null)
if (c == 'q') opt.query = true;
if (args.length == getopt.ind) {
print("Usage: paftools.js longcs2seq [-q] <long-cs.paf>");
return;
}
var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g
var buf = new Bytes();
var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
var m, cs = null, t = buf.toString().split("\t");
for (var i = 12; i < t.length; ++i)
if ((m = /^cs:Z:(\S+)/.exec(t[i])) != null) {
cs = m[1];
break;
}
if (cs == null) continue;
var ts = "", qs = "";
while ((m = re_cs.exec(cs)) != null) {
if (m[1] == "=") ts += m[2], qs += m[2];
else if (m[1] == "+") qs += m[2].toUpperCase();
else if (m[1] == "-") ts += m[2].toUpperCase();
else if (m[1] == "*") ts += m[2][0].toUpperCase(), qs += m[2][1].toUpperCase();
else if (m[1] == ":") throw Error("Long cs is required");
}
if (opt.query) {
print(">" + t[0] + "_" + t[2] + "_" + t[3]);
print(qs);
} else {
print(">" + t[5] + "_" + t[7] + "_" + t[8]);
print(ts);
}
}
file.close();
buf.destroy();
}
/************************* /*************************
***** main function ***** ***** main function *****
*************************/ *************************/
@ -3124,6 +3163,7 @@ function main(args)
print(" sam2paf convert SAM to PAF"); print(" sam2paf convert SAM to PAF");
print(" delta2paf convert MUMmer's delta to PAF"); print(" delta2paf convert MUMmer's delta to PAF");
print(" gff2bed convert GTF/GFF3 to BED12"); print(" gff2bed convert GTF/GFF3 to BED12");
print(" longcs2seq convert long-cs PAF to sequences");
print(""); print("");
print(" stat collect basic mapping information in PAF/SAM"); print(" stat collect basic mapping information in PAF/SAM");
print(" asmstat collect basic assembly information"); print(" asmstat collect basic assembly information");
@ -3168,6 +3208,7 @@ function main(args)
else if (cmd == 'vcfstat') paf_vcfstat(args); else if (cmd == 'vcfstat') paf_vcfstat(args);
else if (cmd == 'sveval') paf_sveval(args); else if (cmd == 'sveval') paf_sveval(args);
else if (cmd == 'vcfsel') paf_vcfsel(args); else if (cmd == 'vcfsel') paf_vcfsel(args);
else if (cmd == 'longcs2seq') paf_longcs2seq(args);
else if (cmd == 'version') print(paftools_version); else if (cmd == 'version') print(paftools_version);
else throw Error("unrecognized command: " + cmd); else throw Error("unrecognized command: " + cmd);
} }