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WANGQ / App-Egaz-0.2.9 / script / egaz 

            

              
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#!/usr/bin/perl
use strict;
use warnings;
use App::Egaz;
App::Egaz->run;
=head1 OVERVIEW
For help with App::Egaz, run "egaz help"
=cut
__END__
minil install --notest && minil clean -y
FAKE_RELEASE=1 minil release
perl -I lib/ script/egaz help
lastz t/pseudocat.fa t/pseudopig.fa > t/default.lav
lavToPsl t/default.lav t/default.psl
perl -I lib/ script/egaz exactmatch t/pig2.fa t/pseudopig.fa --debug
perl -I lib/ t/03-exactmatch.t
perl -I lib/ script/egaz lav2axt t/default.lav
perl -I lib/ t/04-lav2axt.t
perl -I lib/ script/egaz lav2psl t/default.lav
perl -I lib/ t/05-lav2psl.t
perl -I lib/ script/egaz formats
perl -I lib/ t/06-formats.t
perl -I lib/ t/07-maskfasta.t
perl -I lib/ script/egaz partition
perl -I lib/ t/09-partition.t
touch 't/pseudocat.fa[5001,10100]'
lastz 't/pseudocat.fa[5001,10100]' t/pseudopig.fa > t/partition.t.lav
cat t/partition.t.lav | perl ~/Downloads/blastz-normalizeLav 18803 0 > t/partition.t.norm.lav
touch 't/pig2.fa[10001,18000]'
lastz t/pseudocat.fa 't/pig2.fa[10001,18000]' > t/partition.q.lav
cat t/partition.q.lav | perl ~/Downloads/blastz-normalizeLav 18803 22929 > t/partition.q.norm.lav
perl -I lib/ script/egaz normalize t/partition.t.lav --tlen 18803
perl -I lib/ t/10-normalize.t
perl -I lib/ script/egaz raxml t/YDL184C.fas --verbose
perl -I lib/ script/egaz raxml t/YDL184C.fas --seed 999 --tmp . --outgroup Spar -o t/YDL184C.nwk
perl -I lib/ t/11-raxml.t
perl -I lib/ script/egaz blastn t/pig2.fa t/pseudopig.fa --verbose -o t/pig2.blast
perl -I lib/ t/13-blastn.t
egaz partition t/pseudocat/cat.fa --chunk 10000 --overlap 100
egaz partition t/pseudopig/pig1.fa --chunk 10000 --overlap 0
egaz partition t/pseudopig/pig2.fa --chunk 10000 --overlap 0
perl -I lib/ script/egaz lastz t/pseudocat.fa t/pseudopig.fa -v
perl -I lib/ t/14-lastz.t
perl -I lib/ script/egaz prepseq t/pseudopig.fa -v
perl -I lib/ t/15-prepseq.t
perl -I lib/ script/egaz prepseq t/pseudocat.fa -o t/pseudocat
perl -I lib/ script/egaz prepseq t/pseudopig.fa -o t/pseudopig
perl -I lib/ script/egaz lpcnam t/pseudocat t/pseudopig t/default.lav -o t/lpcnam -v
perl -I lib/ script/egaz lpcnam t/pseudocat t/pseudopig t/lav.tar.gz -o t/lpcnam -v
rm -fr t/lpcnam
perl -I lib/ t/16-lpcnam.t
perl -I lib/ script/egaz multiz t/Q_rubravsQ_aliena t/Q_rubravsQ_aquifolioides t/Q_rubravsQ_baronii --tree t/Quercus.nwk
rm -fr Q_rubra_n4
perl -I lib/ t/17-multiz.t
perl -I lib/ script/egaz repeatmasker t/pseudocat.fa -v
perl -I lib/ t/18-repeatmasker.t
perl -I lib/ script/egaz blastmatch t/pig2.blast
perl -I lib/ t/19-blastmatch.t
perl -I lib/ t/20-blastlink.t
perl -I lib/ script/egaz fas2vcf t/YDL184C.fas t/S288c.chr.sizes -v
cat t/example.fas | perl -I lib/ script/egaz fas2vcf \
    stdin t/S288c.chr.sizes --list <(echo -e "S288c\nYJM789") -v
perl -I lib/ t/21-fas2vcf.t
perl -I lib/ script/egaz template t/pseudocat t/pseudopig --multi -o tmp/ -v
perl -I lib/ script/egaz template t/ --prep -o tmp/ --suffix ".fa" --exclude "pig" --perseq t -v
rm -fr tmp/
perl -I lib/ t/91-template.t