BOL: Owner

Script to extract the cluster detail !

BioJoker — Mon, 27 Jul 2020 00:20:25 -0500

$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.1 LTS
Release:	18.04
Codename:	bionic
$ cat /proc/cpuinfo | grep -i 'model name' | head -n 1
model name	: Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz

Split array in Perl !

BioJoker — Sat, 01 Jun 2019 04:23:02 -0500

my @tests = ( ["FOO", "BAR"], ["CRATE", "TRACE"], 
    ["CRATE", "CRATE"], ["TRACE", "CRATE"], 
    ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], );
for my $word_pair (@tests) {
    #Nice way to split the values 
    my ($w1, $w2) = @$word_pair;
    my $simw = simw $w1, $w2;
    say "distance between $w1 and $w2 is: ", 1 - $simw;
}

Perl script to split fasta sequence and create overlaps

BioJoker — Tue, 11 Dec 2018 10:41:14 -0600

#!/usr/bin/perl

use strict;
use warnings;

my $len = 5000;
my $over = 200;
my $seq_id=$ARGV[0];
my $seqFile = $ARGV[1];
my $seq;

open(my $fh, "<", "$seqFile") or die "Can't open < $seqFile: $!";
while (<$fh>) {
    chomp;
    if (m/^>/) { $seq_id = $_; } else { $seq .= $_; }
}

for (my $i = 1; $i <= length $seq; $i += ($len - $over)) {
    my $s = substr ($seq, $i - 1, $len);
    print "$seq_id.($i-", $i + (length $s) - 1, ")\n$s\n";
}

Sync github repo

BioJoker — Sat, 01 Dec 2018 14:55:59 -0600

http://stackoverflow.com/questions/6373277/git-sync-local-repo-with-remote-one

This makes your local repo exactly like your remote repo.
Remember to replace origin and master with the remote and branch that you want to synchronize with.

git fetch origin
git reset --hard origin/master
git clean -f -d