better CLI; more comments
This commit is contained in:
Heng Li
parent
4bc01e90c8
commit
40c4a6ffe1
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@ -1,6 +1,72 @@
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var fuzzy = 3, min_qal = 100, drop_thres = 7;
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/*****************************************************************
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* The K8 Javascript interpreter is required to run this script. *
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* *
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* Source code: https://github.com/attractivechaos/k8 *
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* Binary: http://sourceforge.net/projects/lh3/files/k8/ *
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*****************************************************************/
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var file = arguments.length == 0? new File () : new File(arguments[0]);
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var getopt = function(args, ostr) {
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var oli; // option letter list index
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if (typeof(getopt.place) == 'undefined')
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getopt.ind = 0, getopt.arg = null, getopt.place = -1;
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if (getopt.place == -1) { // update scanning pointer
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if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
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getopt.place = -1;
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return null;
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}
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if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
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++getopt.ind;
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getopt.place = -1;
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return null;
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}
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}
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var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
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if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
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if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
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if (getopt.place < 0) ++getopt.ind;
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return '?';
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}
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if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
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getopt.arg = null;
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if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
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} else { // need an argument
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if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
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getopt.arg = args[getopt.ind].substr(getopt.place);
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else if (args.length <= ++getopt.ind) { // no arg
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getopt.place = -1;
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if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
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return '?';
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} else getopt.arg = args[getopt.ind]; // white space
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getopt.place = -1;
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++getopt.ind;
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}
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return optopt;
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}
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/*********************
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*** Main function ***
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*********************/
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var c, fuzzy = 1, min_qal = 100, drop_thres = 7;
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// parse command line options
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while ((c = getopt(arguments, "f:m:d:")) != null) {
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if (c == 'f') fuzzy = parseInt(getopt.arg);
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else if (c == 'm') min_qal = parseInt(getopt.arg);
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else if (c == 'd') drop_thres = parseInt(getopt.arg);
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}
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if (arguments.length == getopt.ind) {
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print("");
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print("Usage: k8 bwa-typeHLA.js [options] <HLA-to-contig.sam>\n");
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print("Options: -d INT drop a contig if the edit distance to the closest gene is >INT ["+drop_thres+"]");
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print(" -m INT ignore a hit if the gene sequence in the alignment is <INT ["+min_qal+"]");
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print(" -f INT output genotypes whose edit distance is within INT from the best ["+fuzzy+"]");
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print("");
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exit(1);
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}
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// read alignments
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var file = new File(arguments[getopt.ind]);
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var buf = new Bytes();
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var re_cigar = /(\d+)([MIDSH])/g;
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@ -8,11 +74,13 @@ var len = {}, list = [], gcnt = [];
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while (file.readline(buf) >= 0) {
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var m, mm, line = buf.toString();
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var t = line.split("\t");
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// SAM header
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if (t[0].charAt(0) == '@') {
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if (t[0] == '@SQ' && (m = /LN:(\d+)/.exec(line)) != null && (mm = /SN:(\S+)/.exec(line)) != null)
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len[mm[1]] = parseInt(m[1]);
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continue;
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}
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// parse gene name and exon number
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var gene = null, exon = null;
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if ((m = /^(HLA-[^\s_]+)_(\d+)/.exec(t[0])) != null) {
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gene = m[1], exon = parseInt(m[2]) - 1;
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@ -20,6 +88,7 @@ while (file.readline(buf) >= 0) {
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gcnt[exon][gene] = true;
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}
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if (gene == null || exon == null || t[2] == '*') continue;
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// parse clipping and aligned length
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var x = 0, ts = parseInt(t[3]) - 1, te = ts, clip = [0, 0];
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while ((m = re_cigar.exec(t[5])) != null) {
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var l = parseInt(m[1]);
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@ -33,16 +102,17 @@ while (file.readline(buf) >= 0) {
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var left = ts < clip[0]? ts : clip[0];
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var right = tl - te < clip[1]? tl - te : clip[1];
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var nm = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
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list.push([t[2], gene, exon, ts, te, nm, left + right]);
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list.push([t[2], gene, exon, ts, te, nm, left + right]); // left+right should be 0 given a prefix-suffix alignment
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}
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buf.destroy();
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file.close();
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// identify the primary exon(s)
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// identify the primary exons, the exons associated with most genes
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var pri_exon = [], n_pri_exons;
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{
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var cnt = [], max = 0;
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// count the number of genes per exon and track the max
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for (var e = 0; e < gcnt.length; ++e) {
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if (gcnt[e] != null) {
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var c = 0, h = gcnt[e];
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@ -51,6 +121,7 @@ var pri_exon = [], n_pri_exons;
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max = max > c? max : c;
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} else cnt[e] = 0;
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}
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// find primary exons
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var pri_list = [];
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for (var e = 0; e < cnt.length; ++e) {
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if (cnt[e] == max) pri_list.push(e + 1);
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@ -76,7 +147,7 @@ for (var i = 0; i < list.length; ++i) {
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elist[g][list[i][2]] = true;
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}
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// change to the per-exon representation
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// reorganize hits to exons
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var exons = [];
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for (var i = 0; i < list.length; ++i) {
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var li = list[i];
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@ -94,10 +165,9 @@ for (var i = 0; i < glist.length; ++i) {
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// type each exon
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for (var e = 0; e < exons.length; ++e) {
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//for (var e = 1; e < 3; ++e) {
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if (exons[e] == null) continue;
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var ee = exons[e];
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// find good contigs and alleles that have good matches
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// find contigs and genes associated with the current exon
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var ch = {}, gh = {};
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for (var i = 0; i < ee.length; ++i) {
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if (elist[ee[i][1]][e] != null)
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@ -108,7 +178,7 @@ for (var e = 0; e < exons.length; ++e) {
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for (var g in gh) ga.push(parseInt(g));
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var named_ca = [];
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for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]);
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warn("Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(",")+ "])...");
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warn("Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
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// convert representation again
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var sc = [];
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for (var i = 0; i < ee.length; ++i) {
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