acomjean

#Usefull Linux hint

Skip the first line of a file

tail -n +2 file.log

re order columns in file (cut maintains order) tab delimited

awk -F'\t' -v OFS="\t" '{ print $2, $5 }' input.tsv > output.tsv

acomjean

acomjean

#Author: Aram Comjean  Dec/ 2015

#http://stackoverflow.com/questions/6667201/how-to-define-two-dimensional-array-in-python
Lookup = [[0 for x in range(50)] for x in range(50)]

def alignment_paths (x,y):

    #if we have a 1x1 matrix or are at the left or top edge, there is one path
    if (x == 0 or y == 0):
        return 1;

acomjean

import random
from Bio import Entrez
from Bio import SeqIO

#Author: Aram Comjean
#Date: Nov/ 2015
#Hungtington's Disease CAG count


# returns random nucleotide sequence with at least the number of "cag" repeats specified

acomjean

import random;

#Author: Michael Thomas/ Aram Comjean
#Date: Nov/ 2015
#Hungtington's Disease CAG count


# generates random sequence with at least the number of "cag" repeats specified

def generate_random_seq (number_cag_repeats):

acomjean

#Python Problem 1
#reverseComplement.py
#Introduction to Bioinformatics Assignment 2
#Purpose:  reverse compliment
#Your Name: Aram Comjean
#Date: 10/11/2105

#s1 is the string you should use to generate a reverse complement sequence
#Note that your result needs to be presented in the 5' to 3' direction

acomjean

-- Retrieve descendants
-- ====================
-- retrieve descendants of #4

SELECT c.*
FROM Comments AS c
  JOIN TreePaths AS t ON c.comment_id = t.descendant
WHERE t.ancestor = 4;

-- Retrieve ancestors

acomjean

<?php defined('SYSPATH') or die('No direct script access.');
/**
 * MySQL "Closure Table" for Kohana based on Bill Karwin design.
 * 
 * @link  http://www.slideshare.net/billkarwin/models-for-hierarchical-data 
 * @TODO  improve
 * 
 * sql schema:
 * CREATE TABLE `closures` (
 *   `id` int(11) NOT NULL AUTO_INCREMENT,