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

#!/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

#!/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

# 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/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

##################################
#    INTRO 
#
#################################


## ggplot2 tutorial by Adam Wespiser
# August 29, 2013
# download R from: http://www.r-project.org/
# ggplot2 documentation: http://docs.ggplot2.org/

adamwespiser

# Copyright (c) 2012 the authors listed at the following URL, and/or
# the authors of referenced articles or incorporated external code:
# 
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:

adamwespiser

Solution to rosalind's "CORR" problem. 
http://rosalind.info/problems/corr/
The problem is: 
Given a collection of reads(same size), a read is either: 
    1) Correct, and is the same as another read or its reverse trans 
    2) Incorrect by a point mutation, and the thus one base pair difference between the read and a correct read. (Hamming distance = 1) 
report incorrect reads and their correct counterparts. 

There is a strong assumption that a read must be either correct or incorrect, and that all incorrect reads map to at least one correct read. 

adamwespiser

Problem: Given a set of string, find the shortest common superstring such that every string is a subset of the superstring. 


http://rosalind.info/problems/long/ is the location of the problem
http://www.cs.hunter.cuny.edu/~saad/courses/compbio/lectures/lecture15.pdf is a good resource on how to solve the problem, also 
"Approximation Algorithms" by Vazirani. 


Usage: python long.py --file [input seq file] 

adamwespiser

class Dna:
	''' Object representing a FASTA record. '''
	def __init__(self, header, sequence):
		self.head = header
		self.seq = sequence
	def __str__(self, separator=''):
		return ">{0}\n{1}".format(self.head, separator.join(self.seq))
	def __len__(self):
		return len(''.join(self.seq))