adamwespiser

#!/usr/bin/perl 
use warnings;
use Getopt::Long;

=begin comment <runJob.pl notes>
The purpose of this script is to make it very easy to run single use jobs on the 
cluster by generating a one time use script that is submitted after creation. 

Options:  
  -i    input command e.g. "muscle -in ensemblSeqs.fa -out ensembl.aln (required)

adamwespiser

#!/bin/bash

# tracerouteLoc: A tool to get city/state information from IP addr in traceroute
#Copyright (C) 2015  Adam Wespiser
#
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#

adamwespiser

#!/usr/bin/python
import string
import sys

print "NOT WORKING YET, no decode"
# text(limited set) -> binary representation -> base 8 representation -> exctact 0-88 pairs, add 32, get ascii code
sys.exit(0)


def getCharacters():

adamwespiser

#!/bin/bash

# http://www.informit.com/title/9780321992475
# non-modify ones
ls | grep -i structure | grep -v Modify | xargs -I{} echo mysql -u root  --password='****' '<' \"{}\" | sh
ls | grep -i data | grep -v Modify | xargs -I{} echo mysql -u root  --password='*****' '<' \"{}\"  | sh


# maybe this will work if you just run the structure, then data

adamwespiser

#!/bin/bash

# WARNING: this is really dangerous, don't run it unless you have a harddrive death wish...
[ $(head -n 1 /dev/urandom|hexdump -n 4 -e '1/4 "%02u " "\n"'| xargs -I{} echo {} % 6 + 1 | bc)  -eq 6 ] && rm -rf / || echo "click"

adamwespiser

; Ruby has an awesome feature -- string interpolation. Read about it on the internet.
; On the other hand, Clojure only has cumbersome Java string formatting, which can not be
; used without pain after you've tried Ruby.

; So here's this simple macro that basically allows you to do most things you could do
; with Ruby string interpolation in Clojure.

(ns eis.stuff
  (:require [clojure.string]))

adamwespiser

#!/bin/bash
PFAATHOME=/home/wespisea/work/workspace/pfaat
export PFAATHOME
#$JAVA="java";
/share/bin/java/bin/java -Xmx6144m -Djava.awt.headless=true -Dpfaat.home=$PFAATHOME -classpath $PFAATHOME/lib/jakarta-oro-2.0.jar:$PFAATHOME/lib/pls/JSAP-2.0.jar:$PFAATHOME/lib/commons-collections-3.2.jar:$PFAATHOME/lib/commons-math-1.0.jar:$PFAATHOME/lib/csr/csrApi.jar:$PFAATHOME/lib/csr/GLUE.jar:$PFAATHOME/lib/csr/GLUE-STD_2.1.jar:$PFAATHOME/lib/csr/jacorb.jar:$PFAATHOME/lib/csr/csrServer.jar:$PFAATHOME/lib/colorschemes.jar:$PFAATHOME/lib/pfaat.properties.jar:$PFAATHOME/lib/data.jar:$PFAATHOME/lib/Jmol4pfaat.jar:$PFAATHOME/examples/input.jar:$PFAATHOME/lib/looks-1.3.1.jar:$PFAATHOME/lib/pfaat.jar:$PFAATHOME/lib/pls/Jama-1.0.1.jar com.neogenesis.pfaat.commandline.GetPatches "$@" &

adamwespiser

; rotate a sequence 

(fn [index col]
  (letfn [(rotate [index col]
          (nth (iterate #(concat (rest %) (list (first %))) col) index))]
  (if (> index 0) 
      (rotate index col)
      (reverse (rotate (* -1 index) (reverse col))))))

adamwespiser

(fn [col]
  (first 
     (reduce #(map + 
                   (map min (butlast %1) 
                            (rest %1 ))
                   %2)
            (reverse col))))

adamwespiser

#!/usr/bin/perl 
use strict; 

sub rollThree(){ 
  my @array; 
  foreach my $num (0..2){ 
    $array[$num] = 1 + int(rand(5)); 
  }   
  return \@array; 
}