• Toilet Paper: Anyone who has moved before knows one thing: Books are heavy. Guess what books are made of?…. PAPER! That’s right, the same thing that they use to make toilet paper. I suggest you lighten your toilet paper load. Next time you go to the bath room, make note of how much toilet paper you need. How many times do you wipe? If you average 3-4 wipes, can use only 2 squares per wipe and can estimate you will be going to the bathroom 2 times a day, do some math, figure out how much mountain money you will REALLY need. If you are a guy, congratulations, you can bring less TP. Don’t tell the girls this, they may ask you to carry their tent.
• Deodorant: Seriously? All or some of your backpacking buddies are gonna smell worse than the slums of Manila. Why are you going out our way to smell good? Leave this item at home.
• Camera: Skip it. Don’t worry, one of you buddies will bring a camera especially if you are with a big group. One of them may even carry a tripod, a monopod and so much other camera gear that he is going to need a hip replacement by the age of 35. Don’t be that guy. Plus, think about it: if you are taking all the picture, you won’t be in any of them. My wiser older brother once told me: a picture without a person is postcard. If you want pictures of the scenery, just go on flickr and do a search. Chance are pretty good someone else has been there. Make their image your wallpaper. When your co-workers comes, you can brag about what a great trip you had and how much cooler you are than them. Go ahead, gloat away. You’ve got the wallpaper to back it up.
• Tent: So, you hiked all the way out into the woods so you can sleep INDOORS. Forget that. I have seen someone make a very sustainable shelter out of a rain tarp. You just need to be creative. Cavemen didn’t always make it back to the cave and they didn’t have REI either. What did they do? If the going gets really rough, you can sneak into your buddy’s tent.
• Water: I don’t think I need to ask this but what human do you know that will deny another person water?… and you can always count on others to carry water.

This only some of the great ideas that will be present in my new book on backpacking. Please e-mail to preorder it.

  <FilesMatch "\.(?i:fasta)$">
    ForceType application/x-fasta
    Header set Content-Disposition attachment
  </FilesMatch>
  <FilesMatch "\.(?i:aln)$">
    ForceType application/x-aln
    Header set Content-Disposition attachment
  </FilesMatch>

You will have to enable the apache module “mod_header” for this to work.

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require 'rubygems'
require 'hpricot'
require 'open-uri'
 
#term = '1-YR ARM'
#term = '30-YR Fixed'
term = '15-YR Fixed'
 
doc = Hpricot.parse(open("http://www.hicentral.com/MortgageRates.asp")) 
 
rates = [] 
lender_name = ""
 
(doc/"table"/"table"/"tr").each do | row |
   arr =[]
   (row/"td").each do | cell|  
     arr << cell.inner_html() 
   end
   if arr[1] =~ /15-YR Fixed/
      lender_name = arr[0]
      arr.delete(lender_name) 
      lender_name.sub!('<br />',' - ')
   end
   next unless arr[0] =~ /#{term}/
   lender_data ={} 
   lender_data[:lender_name] = lender_name    
   lender_data[:term] = arr[0] 
   lender_data[:apr] = arr[3].to_f
   rates << lender_data
end
 
5.times do | rank |
  puts "Losest Rate ##{rank+1}"
  row = rates.min{|a,b| a[:apr] <=> b[:apr] } 
  puts "  Name: #{row[:lender_name]}"  
  puts "  Term: #{row[:term]}" 
  puts "  APR: #{row[:apr]}"  
  rates.delete(row)
end

Here’s what’s going on:

• On line 7 you will notice that I am interested in the 15-Year mortgage rate. You can change this value to get the report for the term you want.
• On line 9, the program will download the latest rates from the hicentral.com website and parse the page returning an hpricot doc object.
• From line 14 to 30, the program parses each line in the mortgage rate table. The logic is custom to this table. The table is unusual because the lender name is first cell only on the first line (15-YR Fixed) for each lender. To accommodate this, we match the line that has “15-YR Fixed” in second position and delete the lender name from the array (lines 19-23). We then assign the data to our summary data structure (lines 25-29)
• Finally, we show the top 5 lowest mortgage rates (lines 32-38). To do this we use the Ruby max method (line 34). We delete the current max element so it is not counted in the next loop iteration (line 38).

Thomas Lecklider has a great tutorial on how to use Hpricot called Using Hpricot to Traverse and Parse HTML.

Your commends are welcome. Give some refactoring advice if you like. I have wordpress plugin for pre tag so to write ruby code just do:

<pre lang="ruby">
puts YEAH
</pre>

Pretty common, here’s how you do it:

Perl:

use File::Basename; 
$fullname = "/usr/local/src/perl-5.6.1.tar.gz"; 
$file = basename($fullname);

PHP:

$path = "/home/httpd/html/index.php";
$file = basename($path);

Ruby:

path = "/usr/lib/ruby/site_ruby/1.8/rubygems/version.rb"
File.basename path

Python:

import os.path
path =  "/usr/local/bin/python"
os.path.basename(path)

T-SQL (MsSQL Server):

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CREATE FUNCTION [dbo].[fn_file_basename]
(
	-- Add the parameters for the function here
	@file_path Varchar(255)
)
RETURNS Varchar(255)
AS
BEGIN
    declare @file_basename varchar(255)
    IF charindex('\', @file_path) != 0 
	   set @file_basename= reverse(substring(reverse(@file_path), 1, charindex('\', reverse(@file_path))-1))
	else
	   set @file_basename=@file_path
 
	return @file_basename
END

My brilliant co-worker figured this out. The magic is done on line 11:

reverse(substring(reverse(@file_path), 1, charindex('\', reverse(@file_path))-1))

It reverses the string, find the first occurance of the character ‘\’, takes the substring to that character and the reverses again. How elegant!

1. Download the latest jVi release. Unzip the file in your home directory. This will create the directory nbvi-1.2.6.
2. In the Netbeans menu bar, select Tools | Plugins. Click on the Downloaded tab.
3. Press the “Add Plugin” button. Browse to the nbvi-1.2.6 directory and select the two file: org-netbeans-modules-jvi.nbm and com-raelity-jvi.nbm. You should now have 2 plugins availabe in the downloaded list: jVi Key Bindings and jVi Core.
4. Click Install and then click through the installation process. NetBeans will need to restart.
5. After NetBeans has restarted, from the menu bar, select Tools | Options. Click on the last tab which should be jVi Config.
6. Select the “Buffer Modifications” panel in the jVi Config screen.
7. Make sure the ‘expandtab’ value is checked.
8. Change the value of ’shiftwidth’ to 2.
9. Change the value of ‘tabstop’ to 2.

The last option for setting the tabstop and expandtab are pretty important. If you don’t use these, jVi will insert tabs into your Ruby files. This could cause your co-workers to complain about you ruining the formatting in the project.

Congratuations, jVi is now setup in NetBeans. Enjoy.

This blog entry was written for NetBeans 6.7 and with jVi version 1.2.6.

sudo apt-get install emboss emboss-lib

If don’t already have the BioRuby installed, you will need that too:

sudo gem install bio --no-ri --no-rdoc

Your first ruby script calling Emboss Water from Ruby:

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require 'rubygems'
require 'bio'
test_filename =ARGV.shift
target_filename =ARGV.shift
result = Bio::EMBOSS.run('water', '-asequence', test_filename, '-bsequence', target_filename)

Unforntunately, there is not a nice report result class in BioRuby for Emboss Water so you will have to parse the output yourself. Here’s an example script that finds percent similarity:

require 'rubygems'
require 'bio'
test_filename =ARGV.shift
target_filename =ARGV.shift
result = Bio::EMBOSS.run('water', '-asequence', test_filename, '-bsequence', target_filename)
# result now has the text output of water...
# Here's an example of looping through each line of the result to get the similary:
 
test_seq = ""
target_seq = ""
similarity = ''
 
 
result.split("\n").each do | line |
  # This mean
  if line =~ /^# Aligned_sequences/
    puts "Seq '#{test_seq}' has similarity to Seq '#{target_seq}' of #{similarity}"  unless (test_seq == "" ) && (target_seq == "")
    test_seq = ""
    target_seq = ""
  end
  # Get sequence numbers 
  if line =~ /^# (\d+): (\d+)/
     test_seq  = $2 if $1 == '1'
     target_seq = $2 if $1 == '2'
  end
  # parse similarity
  if line =~ /^# Similarity:.*\((.*)%\)/
    similarity  = $1
  end
end
 
puts "Seq '#{test_seq}' has similarity to Seq '#{target_seq}' of #{similarity}"

Place this in a file called water.rb and run it with frags.fasta and frags1.fasta and the above script will output this.

$ ruby water.rb fastas/frags1.fasta frags.fasta 
Seq '1' has similarity to Seq '1' of 100.0
Seq '1' has similarity to Seq '2' of 96.6
Seq '1' has similarity to Seq '3' of 64.3
Seq '1' has similarity to Seq '4' of 97.9
Seq '1' has similarity to Seq '5' of 96.9
Seq '1' has similarity to Seq '6' of 94.1
Seq '1' has similarity to Seq '7' of 62.5
Seq '1' has similarity to Seq '8' of 61.1
Seq '1' has similarity to Seq '9' of 62.5
Seq '1' has similarity to Seq '10' of 57.1
Seq '1' has similarity to Seq '11' of 57.4
Seq '1' has similarity to Seq '12' of 97.8
Seq '1' has similarity to Seq '13' of 50.0
Seq '1' has similarity to Seq '14' of 62.5
Seq '1' has similarity to Seq '15' of 97.9
Seq '1' has similarity to Seq '16' of 62.5
Seq '1' has similarity to Seq '17' of 59.1
Seq '1' has similarity to Seq '18' of 55.9
Seq '1' has similarity to Seq '19' of 61.9
Seq '1' has similarity to Seq '20' of 60.0
Seq '1' has similarity to Seq '21' of 56.4
Seq '1' has similarity to Seq '22' of 56.2

Water is the worse name for a program, EVER. Because it is impossible to Google…

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module Loveable
  module ClassMethods
    def give_hug
    end
  end
  def self.included(base)
    base.extend(ClassMethods)
  end
end
 
class Person
  include Loveable
 
  give_hug
 
end

I fuzzy as to why a certain Rails genius would suggest it is better to do it this way
(see line 7):

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module Loveable
  module ClassMethods
    def give_hug
    end
  end
  def self.included(base)
    base.send :extend, ClassMethods
  end
end
 
class Person
  include Loveable
 
  give_hug
 
end

Feel free to comment…

sudo gem install ruby-prof rcov --no-ri --no-rdoc

Update your test/test_helper.rb, add:

require 'shoulda/rails'

Install Thoughbot’s Shoulda gem (shoulda-2.10.2 at the time of this writing). Make sure you have added GemCutter as one of your ruby gem sources.

sudo gem install shoulda --no-ri --no-rdoc

Edit your applicaitons main Rakefile and add:

require(File.join(File.dirname(__FILE__), 'config', 'boot'))
require 'rake'
require 'rake/testtask'
require 'rake/rdoctask'
require 'tasks/rails'
require 'shoulda/tasks'
 
def run_coverage(files)
  rm_f "coverage"
  rm_f "coverage.data"
 
  # turn the files we want to run into a  string
  if files.length == 0
    puts "No files were specified for testing"
    return
  end
 
  files = files.join(" ")
 
  if PLATFORM =~ /darwin/
    exclude = '--exclude "gems/*"'
  else
    exclude = '--exclude "rubygems/*"'
  end
 
  rcov = "rcov --rails -Ilib:test --sort coverage --text-report #{exclude}  --aggregate coverage.data"
  cmd = "#{rcov} #{files}"
  puts cmd
  sh cmd
end
namespace :test do
 
  desc "Measures unit, functional, and integration test coverage"
  task :coverage do
    run_coverage Dir["test/**/*.rb"]
  end
 
  namespace :coverage do
    desc "Runs coverage on unit tests"
    task :units do
      run_coverage Dir["test/unit/**/*.rb"]
    end
    desc "Runs coverage on functional tests"
    task :functionals do
      run_coverage Dir["test/functional/**/*.rb"]
    end
    desc "Runs coverage on integration tests"
    task :integration do
      run_coverage Dir["test/integration/**/*.rb"]
    end
  end
end

Checkout your new coverage rake tasks:

rake -T | grep cov

Should show you:

rake test:coverage                        # Measures unit, functional, and integration test coverage
rake test:coverage:functionals            # Runs coverage on functional tests
rake test:coverage:integration            # Runs coverage on integration tests
rake test:coverage:units                  # Runs coverage on unit tests