1. Shell scripts on Pegasus 2
Log into pegasus2 using ssh
To start a job you need a shell script
which shell?
job name
#!/bin/bash
#BSUB -J HIV
#BSUB -e %HIV.err
#BSUB -o %HIV.out
#BSUB -n 1
#BSUB -q general
#BSUB -W 72:00 #
cd ${HOME}/Viruses/HIV/
(../Python/distanceClustering2.py ../human_mint_biogrid_hprd_hint.ppi HIV_targets_HPIDB.txt ../human_essential_genes.txt > HIV_ess) >& HIV_ess.log
file for stderr
file for stdout
number of cores
queue
time allocation
your script

2. Shell scripts on Pegasus 2
submit a job with bsub < script.sh
bjobs
transfer data through
scp into your home directory
scp
into scratch directory
returns the status of current jobs

3. Python
Python is a very simple language, and has a very straightforward syntax.
It encourages programmers to program without boilerplate (prepared) code.
There are two major Python versions, Python 2 and Python 3. Python 2 and 3 are quite different. Python 2 is more widely used and supported. However, Python 3 is more semantically correct, and supports newer features.
For example, one difference between Python 2 and 3 is the print statement. In Python 2, the "print" statement is not a function, and therefore it is invoked without parentheses. However, in Python 3, it is a function, and must be invoked with parentheses.
Our first Python program:
#!/usr/bin/python
print “Hello world!”

4. Intendation
Python uses indentation for blocks, instead of curly braces. Both tabs and spaces are supported, but the standard indentation requires standard Python code to use four spaces. For example:
#!/usr/bin/python
x = 1
if x == 1:
# indented four spaces
print "x is 1."

5. Variables & Types
Numbers - Python supports two types of numbers - integers and floating point numbers.
myint = 7
myfloat = 7.0
myfloat = float(7)
Strings - Strings are defined either with a single quote or a double quotes.
mystring = 'hello’
mystring = “hello”
mystring = "Don't worry about apostrophes"
coercing an int into a float

6. Variables & Types
Simple operators can be executed on numbers and strings:
#!/usr/bin/python
one = 1
two = 2
three = one + two
print three
hello = "hello"
world = "world"
helloworld = hello + " " + world
print helloworld
sum = str(one) + " " + (two)
print sum
coercing an int into a string

7. Variables & Types
Assignments can be done on more than one variable "simultaneously" on the same line like this:
#!/usr/bin/python
a,b = 1,2
print a, b
one = 1
two = 2
hello = "hello"
#would this work?
print one + two + hello
assigning 1 to a and 2 to b

8. Lists
Lists are very similar to arrays. They can contain any type of variable, and they can contain as many variables as you wish. Lists can also be iterated over in a very simple manner.
#!/usr/bin/python
mylist = []
mylist.append(1)
mylist.append(2)
mylist.append(3)
print(mylist[0]) # prints 1
print(mylist[1]) # prints 2
print(mylist[2]) # prints 3
# prints out 1,2,3
for x in mylist:
print x

9. Lists What would happen here? catching errors #!/usr/bin/python
mylist = [1,2,3]
print(mylist[10])
#!/usr/bin/python
mylist = [1,2,3]
try:
print(mylist[10])
except IndexError:
pass
expect an error to occur
catch the error
what to do if the error occurred

10. Basic operators
Just as any other programming languages, the addition, subtraction, multiplication, and division operators can be used with numbers.
#!/usr/bin/python
number = * 3 / 4.0
print number
remainder = 11 % 3
print remainder
squared = 7 ** 2
cubed = 2 ** 3
print squared, cubed
does python follow order of operations?
modulo operation
equivalent to 7*7
equivalent to 2*2*2

11. Basic operators - numbers
Just as any other programming languages, the addition, subtraction, multiplication, and division operators can be used with numbers.
#!/usr/bin/python
number = * 3 / 4.0
print number
remainder = 11 % 3
print remainder
squared = 7 ** 2
cubed = 2 ** 3
print squared, cubed
does python follow order of operations?
modulo operation
equivalent to 7*7
equivalent to 2*2*2