Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix s...max_size = 10000 [Sun Jan 10 16:24:20 2021] Introducing random CNVs with the following parameters: >...1263 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix simuINV [Sun Jan 10 16:30:40 2021] Starting simuG .. [Sun Jan 10 1...1263 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_count 2 -prefix simuTRANS [Sun Jan 10 17:12:58 2021] Starting simuG .. [Sun Ja...1263 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, because it #dep...`'---' wgd Copyright (C) 2018 Arthur Zwaenepoel This program comes with...1255 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; my $sps="human"; # Get one from a NCBI taxonomy database my $dbh = Bio:...$sps); $nam = $dbh->get_taxon(-taxonid => 9606); if(!$nam) { print "Try again with...1224 days ago
Perl script to get all the descendent in a tree !
use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',...1216 days ago
1215 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indigestible)...1215 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been installed in the...1212 days ago
1210 days ago