Documented some k8 scripts; more coming
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Heng Li
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The [K8 Javascript shell][k8] is needed to run Javascripts in this directory.
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Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
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page][k8bin].
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## <a name="started"></a>Getting Started
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```sh
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curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
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cp k8-0.2.4/k8-`uname -s` k8 # or better copy to a directory on PATH
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minimap2 --cs test/MT-*.fa | paf2aln.js - | less # pretty print base alignment
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sam2paf.js aln.sam.gz | less -S # convert SAM to PAF
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gff2bed.js anno.gtf | less -S # convert GTF/GFF3 to BED12
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minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln to BED12
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```
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* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for
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eyeballing. PAF has to be generated with minimap2 option `-S`, which writes
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the aligned sequences to the `cs` tag. An example:
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```sh
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../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin
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```
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## Introduction
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* [mapstat.js](mapstat.js): output basic statistics such as the number of
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non-redundant mapped bases, number of split and secondary alignments and
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number of long gaps. This scripts seamlessly works with both SAM and PAF.
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This directory contains auxiliary scripts for format conversion, mapping
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accuracy evaluation and miscellaneous purposes. These scripts *require*
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the [k8 Javascript shell][k8] to run. On Linux or Mac, you can download
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the precompiled k8 binary with:
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```sh
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curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
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cp k8-0.2.4/k8-`uname -s` k8
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```
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It is highly recommended to copy the executable `k8` to a directory on your
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`PATH` such as `/usr/bin/env` can find them.
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* [sim-pbsim.js](sim-pbsim.js): convert reads simulated with [PBSIM][pbsim] to
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FASTA and encode the true mapping positions to read names in a format like
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`S1_33!chr1!225258409!225267761!-`.
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## Use Cases
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* [sim-eval.js](sim-eval.js): evaluate mapping accuracy for FASTA generated
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with [sim-pbsim.js](sim-pbsim.js) or [sim-mason2.js](sim-mason2.js).
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### paf2aln.js: convert PAF to other formats
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* [sam2paf.js](sam2paf.js): convert SAM to PAF.
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Script [paf2aln.js](paf2aln.js) converts PAF with the [cs tag][cs] to
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[MAF][maf] or BLAST-like output. It only works with minimap2 output generated
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using the `--cs` tag.
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### Evaluating mapping accuracy with simulated reads
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Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim]
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to FASTQ and encodes the true mapping position in the read name in a format like
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`S1_33!chr1!225258409!225267761!-`. Similarly, script
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[sim-mason2.js](sim-mason2.js) converts [mason2][mason2] simulated SAM to
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FASTQ.
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Script [sim-eval.js](sim-eval.js) evaluates mapped SAM/PAF.
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```
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Q 60 32478 0 0.000000000 32478
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Q 22 16 1 0.000030775 32494
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Q 21 43 1 0.000061468 32537
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Q 19 73 1 0.000091996 32610
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Q 14 66 1 0.000122414 32676
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Q 10 27 3 0.000214048 32703
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Q 8 14 1 0.000244521 32717
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Q 7 13 2 0.000305530 32730
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Q 6 46 1 0.000335611 32776
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Q 3 10 1 0.000366010 32786
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Q 2 20 2 0.000426751 32806
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Q 1 248 94 0.003267381 33054
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Q 0 31 17 0.003778147 33085
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U 3
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```
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where each Q-line gives the quality threshold, the number of reads mapped with
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mapping quality equal to or greater than the threshold, number of wrong
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mappings, accumulative mapping error rate and the accumulative number of
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mapped reads. The U-line gives the number of unmapped reads if they are present
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in the SAM file.
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[cs]: https://github.com/lh3/minimap2#cs
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[k8]: https://github.com/attractivechaos/k8
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[k8bin]: https://github.com/attractivechaos/k8/releases
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[maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5
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[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
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[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
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@ -1,3 +1,5 @@
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#!/usr/bin/env k8
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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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@ -99,7 +101,7 @@ function print_bed12(exons, cds_st, cds_en, is_short)
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var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name) "([^"]+)";/g;
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var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g;
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var buf = new Bytes();
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var file = new File(arguments[getopt.ind]);
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var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
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var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
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while (file.readline(buf) >= 0) {
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@ -1,3 +1,5 @@
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#!/usr/bin/env k8
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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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#!/usr/bin/env k8
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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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@ -40,7 +42,7 @@ var c, pri_only = false;
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while ((c = getopt(arguments, "p")) != null)
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if (c == 'p') pri_only = true;
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var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
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var file = arguments.length == getopt.ind || arguments[getopt.ind] == "-"? new File() : new File(arguments[getopt.ind]);
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var buf = new Bytes();
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var re = /(\d+)([MIDSHNX=])/g;
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#!/usr/bin/env k8
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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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@ -44,7 +46,7 @@ while ((c = getopt(arguments, "Q:r:m:c")) != null) {
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else if (c == 'c') cap_short_mapq = true;
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}
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var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
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var file = arguments.length == getopt.ind || arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
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var buf = new Bytes();
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var tot = [], err = [];
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#!/usr/bin/env k8
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Bytes.prototype.reverse = function()
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{
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for (var i = 0; i < this.length>>1; ++i) {
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#!/usr/bin/env k8
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Bytes.prototype.reverse = function()
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{
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for (var i = 0; i < this.length>>1; ++i) {
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#!/usr/bin/env k8
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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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else if (c == 'n') fn_name_conv = getopt.arg;
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}
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if (getopt.ind == args.length) {
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warn("Usage: k8 splice2bed.js <in.paf>");
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warn("Usage: k8 splice2bed.js <in.paf>|<in.sam>");
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exit(1);
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}
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@ -83,7 +85,7 @@ function main(args) {
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file.close();
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}
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var file = new File(args[getopt.ind]);
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var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
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var buf = new Bytes();
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var a = [];
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while (file.readline(buf) >= 0) {
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