Transcript An Introduction to Python and Its Use in Bioinformatics

An Introduction to Python and Its
Use in Bioinformatics
Csc 487/687 Computing
for Bioinformatics
Scopes
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Scopes define the “visibility” of
a variable
Variables defined outside of a
function are visible to all of the
functions within a module (file)
Variables defined within a
function are local to that
function
To make a variable that is
defined within a function
global, use the global keyword
Ex 1:
Ex 2:
x=5
x=5
def fnc():
def fnc():
x=2
global x
print x,
x=2
fnc()
print x,
print x
fnc()
>>> ?
print x
>>> ?
Modules
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Why use?
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Code reuse
System namespace partitioning (avoid name clashes)
Implementing shared services or data
Module
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A file containing Python definitions and statements.
The file name is the module name with the suffix .py
appended
Definitions from a module can be imported into other
modules or into the main module
Modules

How to structure a Program
–
One top-level file

–
Main control flow of program
Zero or more supplemental files known as
modules

Libraries of tools
Modules - Import
 Import – used to gain access
Ex:
contents of file b.py
def spam(text):
print text, 'spam'
contents of file a.py
import b
b.spam('gumby')
to tools in modules
Modules - Import

Within a module, the module's name (as a
string) is available as the value of the global
variable _ _name_ _
–
–
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>>> import b
>>>print b._ _name_ _
?
spam=b.spam
spam(“How are you”)
The Module Search Path
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The current directory
The list of directories specified by the
environment variable PYTHONPATH
When PYTHONPATH is not set, or when the
file is not found there, the search continues
in an installation-dependent default path
Standard Modules
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Python Library Reference
Built into the interpreter
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>>> import sys
>>> sys.ps1
'>>> '
>>> sys.ps2
'... '
>>> sys.ps1 = ‘L> '
L> print ‘Hello!'
Yuck!
L> sys.path.append(“C:\\”)
Python Documentation Sources
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#comments
In-file documentation
The dir function Lists of attributes
available on objects
Docstrings:__doc__
In-file documentation
attached to objects
The Dir() Function
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used to find out which names a module
defines. It returns a sorted list of strings.
dir() does not list the names of built-in
functions and variables. If you want a list of
those, they are defined in the standard
module __builtin__.
The Dir() Function Example
The contents of fibo.py
def fib(n):
a, b = 0, 1
while b < n:
print b,
a, b = b, a+b
def fib2(n):
result = []
a, b = 0, 1
while b < n:
result.appen
d(b)
a, b = b,
a+b
return
result
The Dir() Function Example
>>> import fibo, sys
>>> dir(fibo)
['__name__', 'fib', 'fib2']
>>> dir(sys)
['__displayhook__', '__doc__', '__excepthook__', '__name__',
'__stderr__', '__stdin__', '__stdout__', '_getframe', 'api_version',
'argv', 'builtin_module_names', 'byteorder', 'callstats',
'copyright', 'displayhook', 'exc_clear', 'exc_info', 'exc_type',
'excepthook', 'exec_prefix', 'executable', 'exit',
'getdefaultencoding', 'getdlopenflags', 'getrecursionlimit',
'getrefcount', 'hexversion', 'maxint', 'maxunicode', 'meta_path',
'modules', 'path', 'path_hooks', 'path_importer_cache',
'platform', 'prefix', 'ps1', 'ps2', 'setcheckinterval',
'setdlopenflags', 'setprofile', 'setrecursionlimit', 'settrace',
'stderr', 'stdin', 'stdout', 'version', 'version_info', 'warnoptions']
The Dir() Function Example(2)
>>> import __builtin__
>>> dir(__builtin__)
['ArithmeticError', 'AssertionError', 'AttributeError', 'DeprecationWarning',
'EOFError', 'Ellipsis', 'EnvironmentError', 'Exception', 'False',
'FloatingPointError', 'FutureWarning', 'IOError', 'ImportError', 'IndentationError',
'IndexError', 'KeyError', 'KeyboardInterrupt', 'LookupError', 'MemoryError',
'NameError', 'None', 'NotImplemented', 'NotImplementedError', 'OSError',
'OverflowError', 'OverflowWarning', 'PendingDeprecationWarning',
'ReferenceError', 'RuntimeError', 'RuntimeWarning', 'StandardError',
'StopIteration', 'SyntaxError', 'SyntaxWarning', 'SystemError', 'SystemExit',
'TabError', 'True', 'TypeError', 'UnboundLocalError', 'UnicodeDecodeError',
'UnicodeEncodeError', 'UnicodeError', 'UnicodeTranslateError', 'UserWarning',
'ValueError', 'Warning', 'WindowsError', 'ZeroDivisionError', '_', '__debug__',
'__doc__', '__import__', '__name__', 'abs', 'apply', 'basestring', 'bool', 'buffer',
'callable', 'chr', 'classmethod', 'cmp', 'coerce', 'compile', 'complex', 'copyright',
'credits', 'delattr', 'dict', 'dir', 'divmod', 'enumerate', 'eval', 'execfile', 'exit', 'file',
'filter', 'float', 'frozenset', 'getattr', 'globals', 'hasattr', 'hash', 'help', 'hex', 'id',
'input', 'int', 'intern', 'isinstance', 'issubclass', 'iter', 'len', 'license', 'list', 'locals',
'long', 'map', 'max', 'min', 'object', 'oct', 'open', 'ord', 'pow', 'property', 'quit',
'range', 'raw_input', 'reduce', 'reload', 'repr', 'reversed', 'round', 'set', 'setattr',
'slice', 'sorted', 'staticmethod', 'str', 'sum', 'super', 'tuple', 'type', 'unichr',
'unicode', 'vars', 'xrange', 'zip']
Python Docstrings
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Provide a convenient way of associating
documentation with Python modules, functions,
classes, and methods.
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An object's docsting is defined by including a string
constant as the first statement in the object's
definition.

Docstrings can be accessed from the interpreter and
from Python programs using the "__doc__" attribute
DocString Example
Ex: b.py
# Internal comment
"""Module Docstring comment """
def fn():
"""Function Docstring comment """
>>> print b.__doc__
Module Docstring comment
>>> print b.fn.__doc__
Function Doctring comment
Class Definition Syntax
class ClassName:
<statement-1>
...
<statement-N>
Class Objects
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Attribute references
–
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Valid attribute names are all the names that were
in the class's namespace when the class object
was created.
Instantiation
uses function notation
Just pretend that the class object is a parameterless
function that returns a new instance of the class
Inheritance
class DerivedClassName(BaseClassName):
<statement-1>
...
<statement-N>

The name BaseClassName must be defined in a scope
containing the derived class definition

class DerivedClassName(modname.BaseClassName):
Multiple Inheritance
class DerivedClassName(Base1, Base2, Base3):
<statement-1>
...
<statement-N>
Iterators
for element in [1, 2, 3]:
print element
for element in (1, 2, 3):
print element
for key in {'one':1, 'two':2}:
print key
for char in "123":
print char
for line in open("myfile.txt"):
print line
Iterators
>>> s = 'abc'
>>> it = iter(s)
>>> it
<iterator object at 0x00A1DB50>
>>> it.next()
'a‘
>>> it.next()
'b‘
>>> it.next()
'c‘
>>> it.next()
Traceback (most recent call last): File "<stdin>", line 1, in ?
it.next()
StopIteration
Debugging
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Can use print statements to “manually”
debug
Can use debugger in PythonWin