OVERVIEW
OF
PYTHON
PYTHON
FOR
GENOMIC
DATA
SCIENCE
Image credit: XKCD, at http://xkcd.com/353/
Who
is
This
Course
For?
No
prior
knowledge
expected:
intended
for
students
with
no
experience
in
programming
whatsoever.
For
you:
oriented
towards
programming
tasks
for
molecular
biology.
Why
Would
You
Want
To
Program?
Images courtesy of http://abstrusegoose.com/ under a Creative Commons license.
Approaches
to
Learning
How
To
Program
Take
a
class
like
this
that
teaches
you
the
basics
Read
a
programming
book
Find
a
program
written
by
somebody
else
and
try
to
understand
it
Ask
an
expert!
Programming
Strategies*
1. Identify
the
required
inputs,
such
as
data
or
speciTications
2.
3.
4.
5.
from
the
user.
Make
an
overall
design
for
the
program,
including
listing
all
the
steps
by
which
the
program
computes
the
output.
Decide
what
will
be
the
output
of
the
program:
will
the
result
be
in
a
Tile,
or
displayed
on
the
screen?
ReTine
the
overall
design
by
specifying
more
detail.
Write
the
program.
* Adapted from Beginning Perl for Bioinformatics by James Tisdall, Published by O'Reilly Media, Inc., 2001
Designing
a
Program
Write
pseudocode
for
a
program
that
computes
the
GC
percentage
composition
of
a
DNA
sequence:
read DNA sequence from user
count the number of Cs in DNA sequence
count the number of Gs in DNA sequence
determine the length of the DNA sequence
compute the GC%
print GC%
6
What
is
Python?
Python
is
not
What
is
Python?
Python
is
an
easy
to
learn,
powerful
programming
language
It
has
efTicient
data
structures
and
a
simple
but
effective
approach
to
object-oriented
programming
It
is
interpreted!
a
compiled
program
is
converted
from
source
code
into
machine-
language
instructions
by
a
compiler,
and
then
run
from
its
binary
form
an
interpreted
program
takes
the
code
you
wrote
and
converts
it
to
binary
on
the
Tly
each
time
you
run
it.
This
is
slower.
9
History
of
Python
Python
was
conceived
and
developed
in
the
late
1980s
and
early
1990s
by
Guido
van
Rossum
at
the
National
Research
Institute
for
Mathematics
and
Computer
Science
in
the
Netherlands.
Python
version
1.0
was
released
in
January
1994.
Python's
core
syntax
and
certain
aspects
of
its
philosophy
are
directly
inherited
from
the
language
ABC,
but
Python
is
also
inTluenced
by
Modula-3,
C,
C++,
Perl,
Java,
the
Unix
shell,
and
other
scripting
languages.
Python
2.0
was
released
on
16
October
2000.
Python
3.0,
a
major,
backwards-incompatible
release,
was
released
on
3
December
2008.
10
Python
Features
It
is
simple
to
use:
Python
syntax
is
clearly
deTined
which
makes
it
easily
readable.
Programs
written
in
Python
are
typically
much
shorter
than
equivalent
C,
C++,
or
Java
programs.
It
is
interactive:
you
can
write
and
test
your
programs
directly
from
a
terminal
window.
It
has
a
large
standard
library:
Pythons
library
of
built-in
functions
offers
a
wide
range
of
programs
that
are
already
written
for
you.
It
is
portable:
Python
runs
on
many
Unix
variants,
on
Mac
OS,
and
on
Windows.
It
is
extensible:
you
can
use
it
as
an
extension
language
for
applications
that
need
a
programmable
interface.
It
is
scalable:
you
can
use
it
for
very
small
or
very
large
programs.
11
Some
Python
Resources
http://www.python.org
:
the
ofTicial
Python
site
Introduction
to
Programming
using
Python
-http://
www.pasteur.fr/formation/infobio/python/
:
a
programming
course
for
biologists
at
the
Pasteur
Institute
Beginning
Python
for
Bioinformatics
-http://www.onlamp.com/
pub/a/python/2002/10/17/biopython.html
:
a
tutorial
by
Patrick
O'Brien
LearnPython.org
:
an
interactive
Python
tutorial.
Think
Python:
How
to
Think
Like
a
Computer
Scientist
-
http://
www.greenteapress.com/thinkpython/
:
a
free
online
Python
book
by
Allen
B.
Downey
12
Some
Useful
Python
Books
Learning Python
by Mark Lutz
Python Programming Python Programming
by John Zelle
for the Absolute
Beginner
by Michael Dawson
Python Cookbook
by David Beazley
and Brian K. Jones
13
Getting
Python
The
most
up-to-date
and
current
source
code,
binaries,
documentation,
news,
etc.
is
available
at
the
ofTicial
website
of
Python:
http://www.python.org/download/
14
Running
the
Python
Interpreter
$
python
Python
2.7.2
(default,
Oct
11
2012,
20:14:37)
[GCC
4.2.1
Compatible
Apple
Clang
4.0
(tags/Apple/
clang-418.0.60)]
on
darwin
Type
"help",
"copyright",
"credits"
or
"license"
for
more
information.
>>>
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