IsmailM

#Dependencies

GeneValidatorApp and GeneValidator have a number of dependencies (including Ruby, Mafft & BLAST) that need to be installed first.

##Ruby (>= 2.0.0)

1. Install Ruby Version Manager

$ curl -sSL https://get.rvm.io | bash -s stable --ruby

IsmailM

require 'bio'

def analyse_input_file(input_file)
  overall_results = []
  biofastafile = Bio::FlatFile.open(Bio::FastaFormat, input_file)
  biofastafile.each_entry do |entry|
    overall_results << analyse_orfs(entry.entry_id, entry.naseq)
  end
  overall_results
end

IsmailM

require 'bio' # you have to install bioruby - gem install bio
require 'fileutils'

# Run by running:
## ruby split_fasta.rb FASTA_FILE MIN MAX OUTPUT_DIR



fasta = ARGV[0]
min = ARGV[1]

IsmailM

function cd_dir_history()
{
    OLDPWD="$PWD"
    echo "# $(date) $USER -> $@" >> "$HISTFILE"

    command cd "$@"

    # If this directory is writable then write to directory-based history file
    # otherwise write history in the usual home-based history file.
    touch "$PWD/.dir_bash_history" 2>/dev/null \

IsmailM

# vim:ft=zsh ts=2 sw=2 sts=2
#
# agnoster's Theme - https://gist.github.com/3712874
# A Powerline-inspired theme for ZSH
#
# # README
#
# In order for this theme to render correctly, you will need a
# [Powerline-patched font](https://gist.github.com/1595572).
#

IsmailM

/*--- waitForKeyElements():  A utility function, for Greasemonkey scripts,
    that detects and handles AJAXed content.

    Usage example:

        waitForKeyElements (
            "div.comments"
            , commentCallbackFunction
        );

IsmailM

require 'rubygems'
require 'sinatra'
require 'omniauth/oauth'

set :sessions, true
set :layout, true

use OmniAuth::Builder do
  provider :twitter, 'key', 'secret'
end

IsmailM

Jekyll is a great tool for building static sites, however, I often see many projects that are including a lot of unused CSS. Since Jekyll generates an entire working site in the _site directory, we can use it to run uncss. Below outlines an example project using uncss and a build.js script.

Note: this assumes you have node and npm installed.

Setting up the project

Firstly, let's set up the project.

jekyll new uncss-example && cd uncss-example

IsmailM

suppressMessages(library("GEOquery")) 
gse <- getGEO('GDS6', GSEMatrix = TRUE)
eset <- GDS2eSet(gse, do.log2 = FALSE)

X <- exprs(eset)  # Get Expression Data

X <- X[rowSums(is.na(X)) != ncol(X),] # remove rows with missing data

knnImputation(X, scale=F)   

IsmailM

# A really really cool method that does extremely important stuff (Careful, don't break it or the world might fall apart)
# x has to be larger than 2)
random <- function(x) {
  n <- sample(1:x, 3) # get 3 random numbers between 1 and x
  results <- list(num1 = n[1],
                  num2 = n[2],
                  num3 = n[3])
  return(results)
}