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

; 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

; 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

(ns bwt.lib) 
(defn pTest [ys]
  (sort-by #(second %) (map vector (range) ys)))

(defn p [ys] 
  (map second (sort-by #(first %) 
                        (map list ys (range)))))

(defn recon[s index]
   (let [l (vec (map first (sort-by #(second %) (map conj (bwt.lib/pTest s)(range)))))

adamwespiser

#!/usr/bin/perl 
use strict; 

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

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

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi
export PATH=/home/wespisea/bin/hmmer/binaries:$PATH:/share/bin:/home/wespisea/bin/blast/bin
alias anto="ssh adam@anto.umassmed.edu"
# User specific aliases and functions
alias pf="cd /home/wespisea/work/research/researchProjects/proteins/patchFinder"

adamwespiser

PS1="\!@local:\W$ "
export CLICOLOR=true
export PATH=$PATH:/Users/dcaffrey/bin:/usr/local/mysql-5.1.41-osx10.5-x86/bin:/Users/dcaffrey/programs/muscle3.6_src:/Users/dcaffrey/programs/ViennaRNA-1.8.3/bin:/Users/dcaffrey/programs/blast-2.2.14/bin:/Users/dcaffrey/programs/hmmer-3.0-macosx-intel/binaries:/Users/dcaffrey/programs/wise2.2.0/src/bin:/Users/dcaffrey/programs/clustalw-2.0.12-macosx/:/Users/dcaffrey/programs/scwrl4:/Users/dcaffrey/programs/meme/bin:/usr/local/mysql/bin/:/Users/dcaffrey/programs/mrbayes/mrbayes-3.1.2:/Users/dcaffrey/programs/usr/local/bin:/Users/dcaffrey/programs/ligplot/hbplus:/Users/dcaffrey/programs/glam-src:/Users/dcaffrey/programs/rosetta3.1Bundles/rosetta_source/bin:/Users/adam/work/scripts/other:/Users/adam/work/scripts/ensembl/modules/:/Users/adam/bin:/Users/adam/work/scripts/other/modules
#PERL5LIB=${PERL5LIB}:/Users/dcaffrey/programs/bioPerl/bioperl-live:/Users/dcaffrey/programs/ensemblApi/ensembl/modules:/Users/dcaffrey/programs/ensemblApi/ensembl-compara/modules:/Users/dcaff

adamwespiser

#!/usr/bin/python 

#    Copyright Adam Wespiser, 2012 
#    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.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of