App-Egaz

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MANIFEST  view on Meta::CPAN

Build.PL
Changes
Dockerfile
LICENSE
META.json
README.md
cpanfile
doc/Karyotype.md
doc/Scer-self.md
doc/Scer.md
doc/fig.multi.png
doc/fig.multi.vsd
lib/App/Egaz.pm
lib/App/Egaz/Command/blastlink.pm
lib/App/Egaz/Command/blastmatch.pm
lib/App/Egaz/Command/blastn.pm
lib/App/Egaz/Command/exactmatch.pm
lib/App/Egaz/Command/fas2vcf.pm
lib/App/Egaz/Command/formats.pm
lib/App/Egaz/Command/lastz.pm
lib/App/Egaz/Command/lav2axt.pm

doc/Scer-self.md  view on Meta::CPAN

# draw the dotplot
cat mm.length.paf |
    tsv-select -f 1-12 |
    rgr field stdin --chr 1 --start 3 --end 4 -a |
    rgr runlist --op overlap -f 13 \
        <(spanr cover mm.filter.rg) \
        stdin |
    tsv-select -f 1-12 \
    > mm.filter.paf

paf2dotplot png medium mm.filter.paf

```

## `wfmash -X`

```shell
cd ~/data/egaz

wfmash -X -p 70 S288c/chr.fasta S288c/chr.fasta > self.paf

paf2dotplot png medium self.paf

```

## blast

```bash
cd ~/data/egaz

mkdir -p S288c_proc
mkdir -p S288c_result

doc/Scer.md  view on Meta::CPAN

### A quick dotplot

```shell
cd ~/data/egaz

brew install wang-q/tap/wfmash
cargo install --git https://github.com/ekg/pafplot --branch main

wfmash S288c/chr.fasta RM11_1a/chr.fasta > aln.paf
paf2dotplot png medium aln.paf

pafplot aln.paf

```

## Template steps

```shell script
cd ~/data/egaz

share/circos.conf.tt2  view on Meta::CPAN

<image>
dir*   = [% dir %]/Circos/[% id %]
file*  = [% id %].circos.png
background*     = white

# radius of inscribed circle in image
radius         = 1500p
background     = white

# by default angle=0 is at 3 o'clock position
angle_offset   = -90

24bit             = yes