adamwespiser

(ns turing.core)

;; define moves 
;; delta(state, symbol) -> (new state, new symbol, direction of movement)
(def m {[:q0 1]  [:q0 1   1], 
        [:q0 0]  [:q1 1   1],
        [:q1 1]  [:q1 1   1],
        [:q1 :B] [:q2 :B -1],
        [:q2 1]  [:q3 0  -1],
        [:q3 1]  [:q3 1  -1],

adamwespiser

# execute the following code to create a theme_publish object 
# for example, ggplot(mtcars,aes(mpg,hp,size=wt))+geom_point()+theme_publish()

# note: for discrete colored data, use gray scale: 
# > palette(gray(0:3 / 3))
# > greys <- palette()

adamwespiser

#!/usr/bin/perl 
use strict;
use warnings;

my $initials = "AW";

my $src = $ARGV[0];
my $trg = $ARGV[1];

$trg =~ s/\/$//g;

adamwespiser

class Dna:
    ''' Object representing a FASTA record. '''
    def __init__(self, header, sequence):
        self.head = header
        self.seq = sequence
    def __repr__(self):
        return '[HTML]' % (self.head)
    def __str__(self, separator=''):
        return '>%s\n%s' % (self.head, separator.join(self.seq))
    def __len__(self):

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))

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

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

# 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

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


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

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)