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

(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

#!/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: