2014年7月25日 星期五

Python virtual environment

Set up Python virtual environment

Install pyenv & pyenv-virtualenv:
$ git clone https://github.com/yyuu/pyenv.git ~/.pyenv
$ git clone https://github.com/yyuu/pyenv-virtualenv.git ~/.pyenv/plugins/pyenv-virtualenv
Add the following to ~/.bash_profile, and source it.
# Python environment 
export PATH=$HOME/.pyenv/bin:$PATH
eval "$(pyenv init -)" 
 
Install Python 2.7
$ pyenv install 2.7.6 
 
Construct Python virtual environment for Galaxy:
$ pyenv virtualenv --no-site-packages 2.7.6 virtualenv
$ pyenv global virtualenv
  • To install the Python modules, run pip install <Module>.
  • To leave the Python virtual environment, run pyenv shell system.
 

2014年7月1日 星期二

Python2 Input and Output

轉錄自:http://en.wikibooks.org/wiki/Python_Programming/Input_and_output

Input[edit]

Note on Python version: The following uses the syntax of Python 2.x. Some of the following is not going to work with Python 3.x.
Python has two functions designed for accepting data directly from the user:
  • input()
  • raw_input()
There are also very simple ways of reading a file and, for stricter control over input, reading from stdin if necessary.

raw_input()[edit]

raw_input() asks the user for a string of data (ended with a newline), and simply returns the string. It can also take an argument, which is displayed as a prompt before the user enters the data. E.g.
print raw_input('What is your name? ')
prints out
What is your name? <user input data here>
Example: in order to assign the user's name, i.e. string data, to a variable "x" you would type
x = raw_input('What is your name?')
Once the user inputs his name, e.g. Simon, you can call it as x
print 'Your name is ' + x
prints out
Your name is Simon
Note:
in 3.x "...raw_input() was renamed to input(). That is, the new input() function reads a line from sys.stdin and returns it with the trailing newline stripped. It raises EOFError if the input is terminated prematurely. To get the old behavior of input(), use eval(input())."

input()[edit]

input() uses raw_input to read a string of data, and then attempts to evaluate it as if it were a Python program, and then returns the value that results. So entering
[1,2,3]
would return a list containing those numbers, just as if it were assigned directly in the Python script.
More complicated expressions are possible. For example, if a script says:
x = input('What are the first 10 perfect squares? ')
it is possible for a user to input:
map(lambda x: x*x, range(10))
which yields the correct answer in list form. Note that no inputted statement can span more than one line.
input() should not be used for anything but the most trivial program. Turning the strings returned from raw_input() into python types using an idiom such as:
x = None
while not x:
    try:
        x = int(raw_input())
    except ValueError:
        print 'Invalid Number'
is preferable, as input() uses eval() to turn a literal into a python type. This will allow a malicious person to run arbitrary code from inside your program trivially.

File Input[edit]

File Objects[edit]

Python includes a built-in file type. Files can be opened by using the file type's constructor:
f = file('test.txt', 'r')
This means f is open for reading. The first argument is the filename and the second parameter is the mode, which can be 'r', 'w', or 'rw', among some others.
The most common way to read from a file is simply to iterate over the lines of the file:
f = open('test.txt', 'r')
for line in f:
    print line[0]
f.close()
This will print the first character of each line. Note that a newline is attached to the end of each line read this way.
The newer and better way to read from a file:
with open("text.txt", "r") as txt:
    for line in txt:
        print line
The advantage is, that the opened file will close itself after reading each line.
Because files are automatically closed when the file object goes out of scope, there is no real need to close them explicitly. So, the loop in the previous code can also be written as:
for line in open('test.txt', 'r'):
    print line[0]
You can read limited numbers of characters at a time like this:
c = f.read(1)
while len(c) > 0:
    if len(c.strip()) > 0: print c,
    c = f.read(1)
This will read the characters from f one at a time, and then print them if they're not whitespace.
A file object implicitly contains a marker to represent the current position. If the file marker should be moved back to the beginning, one can either close the file object and reopen it or just move the marker back to the beginning with:
f.seek(0)

Standard File Objects[edit]

Like many other languages, there are built-in file objects representing standard input, output, and error. These are in the sys module and are called stdin, stdout, and stderr. There are also immutable copies of these in __stdin__, __stdout__, and __stderr__. This is for IDLE and other tools in which the standard files have been changed.
You must import the sys module to use the special stdin, stdout, stderr I/O handles.
import sys
For finer control over input, use sys.stdin.read(). In order to implement the UNIX 'cat' program in Python, you could do something like this:
import sys
for line in sys.stdin:
    print line,
Note that sys.stdin.read() will read from standard input till EOF. (which is usually Ctrl+D.)
Also important is the sys.argv array. sys.argv is an array that contains the command-line arguments passed to the program.
python program.py hello there programmer!
This array can be indexed,and the arguments evaluated. In the above example, sys.argv[2] would contain the string "there", because the name of the program ("program.py") is stored in argv[0]. For more complicated command-line argument processing, see the "argparse" module.

Output[edit]

Note on Python version: The following uses the syntax of Python 2.x. Much of the following is not going to work with Python 3.x. In particular, Python 3.x requires brackets around arguments to "print".
The basic way to do output is the print statement.
print 'Hello, world'
To print multiple things on the same line separated by spaces, use commas between them, like this:
print 'Hello,', 'World'
This will print out the following:
Hello, World
While neither string contained a space, a space was added by the print statement because of the comma between the two objects. Arbitrary data types can be printed this way:
print 1,2,0xff,0777,(10+5j),-0.999,map,sys
This will output the following:
1 2 255 511 (10+5j) -0.999 <built-in function map> <module 'sys' (built-in)>
Objects can be printed on the same line without needing to be on the same line if one puts a comma at the end of a print statement:
for i in range(10):
    print i,
This will output the following:
0 1 2 3 4 5 6 7 8 9
To end the printed line with a newline, add a print statement without any objects.
for i in range(10):
    print i,
print
for i in range(10,20):
    print i,
This will output the following:
0 1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18 19
If the bare print statement were not present, the above output would look like:
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
You can use similar syntax when writing to a file instead of to standard output, like this:
print >> f, 'Hello, world'
This will print to any object that implements write(), which includes file objects.

Omitting newlines[edit]

To avoid adding spaces and newlines between objects output with subsequent print statements, you can do one of the following:
Concatenation: Concatenate the string representations of each object, then later print the whole thing at once.
print str(1)+str(2)+str(0xff)+str(0777)+str(10+5j)+str(-0.999)+str(map)+str(sys)
This will output the following:
12255511(10+5j)-0.999<built-in function map><module 'sys' (built-in)>
Write function: You can make a shorthand for sys.stdout.write and use that for output.
import sys
write = sys.stdout.write
write('20')
write('05\n')
This will output the following:
2005
You may need sys.stdout.flush() to get that text on the screen quickly.

Examples[edit]

Examples of output with Python 2.x:
  • print "Hello"
  • print "Hello", "world"
    • Separates the two words with a space.
  • print "Hello", 34
    • Prints elements of various data types, separating them by a space.
  • print "Hello " + 34
    • Throws an error as a result of trying to concatenate a string and an integer.
  • print "Hello " + str(34)
    • Uses "+" to concatenate strings, after converting a number to a string.
  • print "Hello",
    • Prints "Hello " without a newline, with a space at the end.
  • sys.stdout.write("Hello")
    • Prints "Hello" without a newline. Doing "import sys" is a prerequisite. Needs a subsequent "sys.stdout.flush()" in order to display immediately on the user's screen.
  • sys.stdout.write("Hello\n")
    • Prints "Hello" with a newline.
  • print >> sys.stderr, "An error occurred."
    • Prints to standard error stream.
  • sys.stderr.write("Hello\n")
    • Prints to standard error stream.
  • sum=2+2; print "The sum: %i" % sum
    • Prints a string that has been formatted with the use of an integer passes as an argument.
  • formatted_string = "The sum: %i" % (2+2); print formatted_string
    • Like the previous, just that the formatting happens outside of the print statement.
  • print "Float: %6.3f" % 1.23456
    • Outputs "Float: 1.234". The number 3 after the period specifies the number of decimal digits after the period to be displayed, while 6 before the period specifies the total number of characters the displayed number should take, to be padded with spaces if needed.
  • print "%s is %i years old" % ("John", 23)
    • Passes two arguments to the formatter.
Examples of output with Python 3.x:
  • from __future__ import print_function
    • Ensures Python 2.6 and later Python 2.x can use Python 3.x print function.
  • print ("Hello", "world")
    • Prints the two words separated with a space. Notice the surrounding brackets, ununsed in Python 2.x.
  • print ("Hello world", end="")
    • Prints without the ending newline.
  • print ("Hello", "world", sep="-")
    • Prints the two words separated with a a dash.

File Output[edit]

Printing numbers from 1 to 10 to a file, one per line:
file1 = open("TestFile.txt","w")
for i in range(1,10+1):
  print >>file1, i
file1.close()
With "w", the file is opened for writing. With ">>file", print sends its output to a file rather than standard output.
Printing numbers from 1 to 10 to a file, separated with a dash:
file1 = open("TestFile.txt","w")
for i in range(1,10+1):
  if i>1:
    file1.write("-")
  file1.write(str(i))
file1.close()
Opening a file for appending rather than overwriting:
file1 = open("TestFile.txt","a")
See also Files chapter.