├── ClustersPloter.sh ├── README.md ├── bin ├── ClustersPloter.sh └── svgcleaner ├── data ├── NC_017659.1.fa ├── NC_017659.1.fa.GC ├── NC_017659.1.fa.amb ├── NC_017659.1.fa.ann ├── NC_017659.1.fa.bwa.read1.fastq.gz ├── NC_017659.1.fa.bwa.read2.fastq.gz ├── NC_017659.1.fa.bwa.sh ├── NC_017659.1.fa.bwa.sh.sign ├── NC_017659.1.fa.bwt ├── NC_017659.1.fa.longreads.fa ├── NC_017659.1.fa.longreads.fq.gz ├── NC_017659.1.fa.longreads.map2ref.paf.gz ├── NC_017659.1.fa.longreads.map2ref.sort.bam ├── NC_017659.1.fa.mutations.txt ├── NC_017659.1.fa.mutations.vcf ├── NC_017659.1.fa.nhr ├── NC_017659.1.fa.nin ├── NC_017659.1.fa.nsq ├── NC_017659.1.fa.pac ├── NC_017659.1.fa.sa ├── NC_017659.1.fa.sam.sorted.bam ├── NC_017659.1.fa.sam.sorted.bam.bai ├── NC_017659.1.fa.to.NC_017659.1.fa.blast.m6 ├── NC_017659.1.gff ├── NC_017659.1.indel.fa ├── NC_017659.1.indel.fa.amb ├── NC_017659.1.indel.fa.ann ├── NC_017659.1.indel.fa.bwa.read1.fastq.gz ├── NC_017659.1.indel.fa.bwa.read2.fastq.gz ├── NC_017659.1.indel.fa.bwa.sh ├── NC_017659.1.indel.fa.bwa.sh.sign ├── NC_017659.1.indel.fa.bwt ├── NC_017659.1.indel.fa.longreads.fa ├── NC_017659.1.indel.fa.longreads.fq.gz ├── NC_017659.1.indel.fa.longreads.map2ref.paf.gz ├── NC_017659.1.indel.fa.longreads.map2ref.sort.bam ├── NC_017659.1.indel.fa.longreads.map2ref.sort.bam.bai ├── NC_017659.1.indel.fa.mutations.txt ├── NC_017659.1.indel.fa.mutations.vcf ├── NC_017659.1.indel.fa.pac ├── NC_017659.1.indel.fa.sa ├── NC_017659.1.indel.fa.sam.sorted.bam ├── NC_017659.1.indel.fa.sam.sorted.bam.bai ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6 ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6.common ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam.bai ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.paf.gz ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.bwa.sh ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.bwa.sh.sign ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam ├── NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam.bai ├── NC_017659.1.indel.fa.to.self.m6 ├── NC_017659.1.indel.gff ├── NC_017659.1.reverse.gff ├── base_brand.txt ├── blast.sh ├── blast2commom.sh ├── bwa.sh ├── chr14.fa ├── chr14.fa.length ├── chr14.gff ├── empty.gff ├── hg002.chr14.vcf.gz ├── illumina.chr14.sort.bam ├── illumina.chr14.sort.bam.14.66901400.66902400.depth ├── illumina.chr14.sort.bam.14.66901400.66903400.depth ├── illumina.chr14.sort.bam.bai ├── illumina.chr14.sort.bam.depth.txt ├── indel.sh ├── mummer.delta.filter.coords ├── mummer.sh ├── pacbio.chr14.sort.bam ├── pacbio.chr14.sort.bam.bai ├── paf.sh ├── sam2bam.sort.sh ├── simulate.reads.sh ├── wget.sh └── yeast │ ├── GCF_000146045.2_R64_genomic.empty.gff │ ├── GCF_000146045.2_R64_genomic.fna │ ├── GCF_000146045.2_R64_genomic.gff │ ├── GCF_000146045.2_R64_protein.faa │ └── GCF_000146045.2_R64_rna.fna ├── env.sh ├── example ├── .out2.rep2.html.swp ├── .out7.rep2.html.swp ├── convert.sh ├── diff.sh ├── env.sh ├── feature.color.label.6.conf ├── feature.color.label.6.conf.out6 ├── feature.color.label.6.conf.out8 ├── feature.color.label.7.conf ├── feature.color.label.7.conf.legend.setting.conf ├── feature.color.label.conf.out1 ├── feature.color.label.conf.out2 ├── feature.color.label.conf.out3 ├── feature.color.label.conf.out4 ├── feature.color.label.conf.out5 ├── feature.crossing.link.out1 ├── feature.crossing.link.out2 ├── feature.crossing.link.out3 ├── feature.crossing.link.out4 ├── feature.crossing.link.out5 ├── feature.crossing.link.out6 ├── feature.crossing.link.out8 ├── json.pl ├── log ├── main.1.conf ├── main.1.conf.out1 ├── main.2.conf ├── main.2.conf.out2 ├── main.3.conf ├── main.3.conf.out3 ├── main.3.fullparamater.conf ├── main.4.conf ├── main.4.conf.out4 ├── main.5.conf ├── main.5.conf.out5 ├── main.6.conf ├── main.6.conf.out6 ├── main.7.conf ├── main.7.conf.out7 ├── main.8.conf ├── main.8.conf.out8 ├── main.9.conf ├── myjson.pl ├── myth.pm ├── nohup.out ├── note.txt ├── out.tar.bz2 ├── out1.cat.log ├── out1.cleaned.svg ├── out1.hist_scatter_line.setting.conf ├── out1.html ├── out1.pO83_CORR.1.out1.synteny.gff ├── out1.pO83_CORR.1.out1.synteny.setting.conf ├── out1.pO83_CORR.1.to.pO83_CORR.2.out1.synteny.crosslink ├── out1.pO83_CORR.2.out1.synteny.gff ├── out1.pO83_CORR.2.out1.synteny.setting.conf ├── out1.pO83_CORR.indel.out1.synteny.gff ├── out1.pO83_CORR.indel.out1.synteny.setting.conf ├── out1.pO83_CORR.indel.to.pO83_CORR.out1.synteny.crosslink ├── out1.pO83_CORR.out1.hist_scatter_line.gff ├── out1.pO83_CORR.out1.hist_scatter_line.setting.conf ├── out1.pO83_CORR.out1.synteny.gff ├── out1.pO83_CORR.out1.synteny.setting.conf ├── out1.pO83_CORR.reverse.out1.hist_scatter_line.gff ├── out1.pO83_CORR.reverse.out1.hist_scatter_line.setting.conf ├── out1.plot.error ├── out1.plot.error.tmp ├── out1.plot.log ├── out1.prepare.data.error ├── out1.prepare.data.error.tmp ├── out1.prepare.data.log ├── out1.rep1.html ├── out1.svg ├── out1.synteny.crosslink ├── out1.synteny.setting.conf ├── out2.cairosvg.dpi200.png ├── out2.cairosvg.png ├── out2.cat.log ├── out2.cleaned.cairosvg.pdf ├── out2.cleaned.svg ├── out2.html ├── out2.pO83_CORR.indel.out2.reads_mapping.gff ├── out2.pO83_CORR.indel.out2.reads_mapping.setting.conf ├── out2.pO83_CORR.indel.out2.synteny.gff ├── out2.pO83_CORR.indel.out2.synteny.setting.conf ├── out2.pO83_CORR.indel.to.pO83_CORR.out2.synteny.crosslink ├── out2.pO83_CORR.out2.reads_mapping.crosslink ├── out2.pO83_CORR.out2.reads_mapping.gff ├── out2.pO83_CORR.out2.reads_mapping.setting.conf ├── out2.pO83_CORR.out2.synteny.gff ├── out2.pO83_CORR.out2.synteny.setting.conf ├── out2.pO83_CORR.twin.out2.reads_mapping.crosslink ├── out2.pO83_CORR.twin.out2.reads_mapping.gff ├── out2.pO83_CORR.twin.out2.reads_mapping.setting.conf ├── out2.plot.error ├── out2.plot.error.tmp ├── out2.plot.log ├── out2.png ├── out2.prepare.data.error ├── out2.prepare.data.log ├── out2.reads_mapping.crosslink ├── out2.reads_mapping.setting.conf ├── out2.svg ├── out2.synteny.crosslink ├── out2.synteny.setting.conf ├── out2 │ ├── feature.color.label.conf.out2 │ ├── feature.crossing.link.out2 │ ├── main.2.conf │ ├── main.2.conf.out2 │ ├── out2.cat.log │ ├── out2.html │ ├── out2.notitle.svg │ ├── out2.pO83_CORR.indel.out2.synteny.gff │ ├── out2.pO83_CORR.indel.out2.synteny.setting.conf │ ├── out2.pO83_CORR.indel.to.pO83_CORR.out2.synteny.crosslink │ ├── out2.pO83_CORR.out2.synteny.gff │ ├── out2.pO83_CORR.out2.synteny.setting.conf │ ├── out2.plot.error │ ├── out2.plot.log │ ├── out2.prepare.data.error │ ├── out2.prepare.data.log │ ├── out2.svg │ ├── out2.synteny.crosslink │ ├── out2.synteny.setting.conf │ ├── out22.html │ ├── out22.notitle.svg │ ├── out22.rep1.html │ ├── out22.rep2.html │ ├── out22.rep3.html │ ├── out22.sh │ ├── out22.sh.log │ ├── out22.svg │ ├── plot.genome.featureCluster.pl │ ├── tracks.2.list │ ├── tracks.2.list.out2 │ ├── tracks.2.list.out2.tmp │ ├── x │ ├── x1 │ ├── x2 │ └── x3 ├── out3.cat.log ├── out3.chr14.out3.hist_scatter_line.gff ├── out3.chr14.out3.hist_scatter_line.setting.conf ├── out3.chr14.out3.reads_mapping.crosslink ├── out3.chr14.out3.reads_mapping.gff ├── out3.chr14.out3.reads_mapping.setting.conf ├── out3.cleaned.svg ├── out3.general_features.setting.conf ├── out3.gif ├── out3.hist_scatter_line.setting.conf ├── out3.html ├── out3.notitle.svg ├── out3.plot.error ├── out3.plot.error.tmp ├── out3.plot.log ├── out3.prepare.data.error ├── out3.prepare.data.error.tmp ├── out3.prepare.data.log ├── out3.reads_mapping.crosslink ├── out3.reads_mapping.setting.conf ├── out3.svg ├── out3.yeast.out3.general_features.gff ├── out3.yeast.out3.general_features.setting.conf ├── out4.cat.log ├── out4.cleaned.svg ├── out4.html ├── out4.pO83_CORR.indel.out4.synteny.gff ├── out4.pO83_CORR.indel.out4.synteny.setting.conf ├── out4.pO83_CORR.indel.to.pO83_CORR.out4.synteny.crosslink ├── out4.pO83_CORR.out4.synteny.gff ├── out4.pO83_CORR.out4.synteny.setting.conf ├── out4.plot.error ├── out4.plot.error.tmp ├── out4.plot.log ├── out4.prepare.data.error ├── out4.prepare.data.error.tmp ├── out4.prepare.data.log ├── out4.svg ├── out4.synteny.crosslink ├── out4.synteny.setting.conf ├── out5.cat.log ├── out5.cleaned.svg ├── out5.html ├── out5.pO83_CORR.indel.out5.synteny.gff ├── out5.pO83_CORR.indel.out5.synteny.setting.conf ├── out5.pO83_CORR.indel.to.pO83_CORR.out5.synteny.crosslink ├── out5.pO83_CORR.out5.synteny.gff ├── out5.pO83_CORR.out5.synteny.setting.conf ├── out5.plot.error ├── out5.plot.error.tmp ├── out5.plot.log ├── out5.prepare.data.error ├── out5.prepare.data.error.tmp ├── out5.prepare.data.log ├── out5.svg ├── out5.synteny.crosslink ├── out5.synteny.setting.conf ├── out6.cat.log ├── out6.cleaned.svg ├── out6.html ├── out6.pO83_CORR.indel.out6.synteny.gff ├── out6.pO83_CORR.indel.out6.synteny.setting.conf ├── out6.pO83_CORR.indel.reverse.out6.synteny.gff ├── out6.pO83_CORR.indel.reverse.out6.synteny.setting.conf ├── out6.pO83_CORR.indel.to.pO83_CORR.out6.synteny.crosslink ├── out6.pO83_CORR.indel.twin.out6.synteny.gff ├── out6.pO83_CORR.indel.twin.out6.synteny.setting.conf ├── out6.pO83_CORR.indel.twin.to.pO83_CORR.indel.out6.synteny.crosslink ├── out6.pO83_CORR.indel.twin.to.pO83_CORR.indel.reverse.out6.synteny.crosslink ├── out6.pO83_CORR.out6.synteny.gff ├── out6.pO83_CORR.out6.synteny.setting.conf ├── out6.plot.error ├── out6.plot.error.tmp ├── out6.plot.log ├── out6.prepare.data.error ├── out6.prepare.data.error.tmp ├── out6.prepare.data.log ├── out6.svg ├── out6.synteny.crosslink ├── out6.synteny.setting.conf ├── out7.cleaned.svg ├── out7.html.gz ├── out7.notitle.svg ├── out7.plot.error ├── out7.plot.error.tmp ├── out7.plot.log ├── out7.svg ├── out7 │ ├── try1 │ │ ├── feature.color.label.7.conf │ │ ├── feature.color.label.7.conf.legend.setting.conf │ │ ├── main.7.conf │ │ ├── main.7.conf.out7 │ │ ├── out7.html │ │ ├── out7.notitle.svg │ │ ├── out7.plot.error │ │ ├── out7.plot.log │ │ ├── out7.svg │ │ ├── tracks.7.list │ │ ├── tracks.7.list.out7 │ │ ├── tracks.7.list.out7.out7.legend.gff │ │ ├── tracks.7.list.out7.out7.legend.list │ │ └── work.sh │ └── try2 │ │ ├── feature.color.label.7.conf │ │ ├── feature.color.label.7.conf.legend.setting.conf │ │ ├── main.7.conf │ │ ├── main.7.conf.out7 │ │ ├── out7.html │ │ ├── out7.notitle.svg │ │ ├── out7.plot.error │ │ ├── out7.plot.log │ │ ├── out7.svg │ │ ├── tracks.7.list │ │ ├── tracks.7.list.out7 │ │ ├── tracks.7.list.out7.out7.legend.gff │ │ ├── tracks.7.list.out7.out7.legend.list │ │ └── work.sh ├── out8.cat.log ├── out8.cleaned.svg ├── out8.html ├── out8.pO83_CORR.indel.blast.out8.synteny.gff ├── out8.pO83_CORR.indel.blast.out8.synteny.setting.conf ├── out8.pO83_CORR.indel.blast.to.pO83_CORR.out8.synteny.crosslink ├── out8.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.out8.synteny.crosslink ├── out8.pO83_CORR.out8.synteny.gff ├── out8.pO83_CORR.out8.synteny.setting.conf ├── out8.pO83_CORR.twin.minimap.out8.synteny.gff ├── out8.pO83_CORR.twin.minimap.out8.synteny.setting.conf ├── out8.plot.error ├── out8.plot.error.tmp ├── out8.plot.log ├── out8.prepare.data.error ├── out8.prepare.data.error.tmp ├── out8.prepare.data.log ├── out8.svg ├── out8.synteny.crosslink ├── out8.synteny.setting.conf ├── plot.genome.featureCluster.pl ├── prepare.data.pl ├── rep.sh ├── srmy ├── tmp ├── tmp.svg ├── tracks.1.list ├── tracks.1.list.out1 ├── tracks.1.list.out1.tmp ├── tracks.2.list ├── tracks.2.list.out2 ├── tracks.2.list.out2.tmp ├── tracks.3.list ├── tracks.3.list.out3 ├── tracks.3.list.out3.tmp ├── tracks.4.list ├── tracks.4.list.out4 ├── tracks.4.list.out4.tmp ├── tracks.5.list ├── tracks.5.list.out5 ├── tracks.5.list.out5.tmp ├── tracks.6.list ├── tracks.6.list.out6 ├── tracks.6.list.out6.tmp ├── tracks.7.list ├── tracks.7.list.out7 ├── tracks.7.list.out7.out7.legend.gff ├── tracks.7.list.out7.out7.legend.list ├── tracks.8.list ├── tracks.8.list.out8 ├── tracks.8.list.out8.tmp ├── tracks.9.list ├── work.sh ├── work.sh.err ├── x └── xx ├── example_old ├── .setting.conf ├── clean.sh ├── out.cleaned.svg ├── out10.svg ├── out11.cleaned.svg ├── out11.svg ├── out2.cleaned.svg ├── out3.1.cleaned.svg ├── out3.2.cleaned.svg ├── out3.cleaned.svg ├── out7.cleaned.svg ├── out8.cleaned.svg └── out9.cleaned.svg ├── git.rm.sh ├── git.sh ├── src ├── JSON.pm ├── Times_New_Roman.ttf ├── d3-transform.js ├── d3.v5.js ├── gff_to_bam.pl ├── modify_feature.js ├── myth.pm ├── myth.pm.190725 ├── navigator ├── plot.genome.featureCluster.pl ├── prepare.data.pl ├── svg-pan-zoom.js ├── text_height_width_by_size.json ├── text_height_width_by_size.pl └── xx │ └── lib64 │ └── perl5 │ ├── Imager.pm │ ├── Imager │ ├── API.pod │ ├── APIRef.pod │ ├── Color.pm │ ├── Color │ │ ├── Float.pm │ │ └── Table.pm │ ├── Cookbook.pod │ ├── CountColor.pm │ ├── Draw.pod │ ├── Engines.pod │ ├── Expr.pm │ ├── Expr │ │ └── Assem.pm │ ├── ExtUtils.pm │ ├── File │ │ ├── CUR.pm │ │ ├── ICO.pm │ │ ├── PNG.pm │ │ ├── SGI.pm │ │ └── TIFF.pm │ ├── Files.pod │ ├── Fill.pm │ ├── Filter │ │ ├── DynTest.pm │ │ ├── Flines.pm │ │ └── Mandelbrot.pm │ ├── Filters.pod │ ├── Font.pm │ ├── Font │ │ ├── BBox.pm │ │ ├── FT2.pm │ │ ├── FreeType2.pm │ │ ├── Image.pm │ │ ├── Test.pm │ │ ├── Truetype.pm │ │ ├── Type1.pm │ │ ├── W32.pm │ │ └── Wrap.pm │ ├── Fountain.pm │ ├── Handy.pod │ ├── IO.pod │ ├── ImageTypes.pod │ ├── Inline.pod │ ├── Install.pod │ ├── LargeSamples.pod │ ├── Matrix2d.pm │ ├── Preprocess.pm │ ├── Probe.pm │ ├── Regops.pm │ ├── Security.pod │ ├── Test.pm │ ├── Threads.pod │ ├── Transform.pm │ ├── Transformations.pod │ ├── Tutorial.pod │ ├── include │ │ ├── draw.h │ │ ├── dynaload.h │ │ ├── ext.h │ │ ├── feat.h │ │ ├── imager.h │ │ ├── imageri.h │ │ ├── imconfig.h │ │ ├── imdatatypes.h │ │ ├── imerror.h │ │ ├── imexif.h │ │ ├── imext.h │ │ ├── imextdef.h │ │ ├── imextpl.h │ │ ├── imextpltypes.h │ │ ├── imexttypes.h │ │ ├── imio.h │ │ ├── immacros.h │ │ ├── imperl.h │ │ ├── imperlio.h │ │ ├── imrender.h │ │ ├── iolayer.h │ │ ├── iolayert.h │ │ ├── log.h │ │ ├── plug.h │ │ ├── ppport.h │ │ ├── regmach.h │ │ ├── rendert.h │ │ └── stackmach.h │ ├── interface.pod │ ├── regmach.pod │ └── typemap │ ├── auto │ └── Imager │ │ ├── .packlist │ │ ├── CountColor │ │ └── CountColor.so │ │ ├── File │ │ ├── ICO │ │ │ └── ICO.so │ │ ├── PNG │ │ │ └── PNG.so │ │ ├── SGI │ │ │ └── SGI.so │ │ └── TIFF │ │ │ └── TIFF.so │ │ ├── Filter │ │ ├── DynTest │ │ │ └── DynTest.so │ │ ├── Flines │ │ │ └── Flines.so │ │ └── Mandelbrot │ │ │ └── Mandelbrot.so │ │ ├── Font │ │ └── FT2 │ │ │ └── FT2.so │ │ └── Imager.so │ └── perllocal.pod └── wiki ├── B1 ├── README.md ├── chr1.fa.length ├── chr1.gff ├── myfeature_setting.txt ├── mymain.conf ├── mymain.conf.out1 ├── mytrack.list ├── mytrack.list.out1 ├── out1.html ├── out1.notitle.svg ├── out1.plot.error ├── out1.plot.error.tmp ├── out1.plot.log ├── out1.svg ├── test.sh └── work.sh └── README.md /ClustersPloter.sh: -------------------------------------------------------------------------------- 1 | bin/ClustersPloter.sh -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orangeSi/GSSplayground/HEAD/README.md -------------------------------------------------------------------------------- /bin/ClustersPloter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orangeSi/GSSplayground/HEAD/bin/ClustersPloter.sh -------------------------------------------------------------------------------- /bin/svgcleaner: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orangeSi/GSSplayground/HEAD/bin/svgcleaner -------------------------------------------------------------------------------- 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