File input and output if-then-else

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File input and outputif-then-else

• Genome 559 Introduction to Statistical and
  Computational Genomics
• Prof. William Stafford Noble

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File input and output
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Opening files

• The open() command returns a file object.
• ltfilehandlegt open(ltfilenamegt, ltaccess typegt)
• Python can read, write or append to a file
• 'r' read
• 'w' write
• 'a' append
• Create a file called hello.txt containing one
  line Hello, world!
• gtgtgt myFile open("hello.txt", "r")

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Reading the whole file

• You can read the contents of the file into a
  single string.
• gtgtgt myString myFile.read()
• gtgtgt print myString
• Hello, world!
• gtgtgt

Why is there a blank line here?
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Reading the whole file

• Now add a second line to your file (How ya
  doin?) and try again.
• gtgtgt myFile open("hello.txt", "r")
• gtgtgt myString myFile.read()
• gtgtgt print myString
• Hello, world!
• How ya doin'?
• gtgtgt

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Reading the whole file

• Alternatively, you can read the file into a list
  of strings.
• gtgtgt myFile open("hello.txt", "r")
• gtgtgt myStringList myFile.readlines()
• gtgtgt print myStringList
• 'Hello, world!\n', "How ya doin'?\n"
• gtgtgt print myStringList1
• How ya doin'?

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Reading one line at a time

• The readlines() command puts all the lines into a
  list of strings.
• The readline() command returns the next line.
• gtgtgt myFile open("hello.txt", "r")
• gtgtgt myString myFile.readline()
• gtgtgt print myString
• Hello, world!
• gtgtgt myString myFile.readline()
• gtgtgt print myString
• How ya doin'?
• gtgtgt

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Writing to a file

• Open the file for writing or appending.
• gtgtgt myFile open("new.txt", "w")
• Use the ltfilegt.write() method.
• gtgtgt myFile.write("This is a new file\n")
• gtgtgt myFile.close()
• gtgtgt D
• gt cat new.txt
• This is a new file

Always close a file after you are finished
reading from or writing to it.
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Print vs write

• ltfilegt.write() does not automatically append an
  end-of-line character.
• ltfilegt.write() requires a string as input
• gtgtgt newFile.write("foo")
• gtgtgt newFile.write(1)
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• TypeError argument 1 must be string or read-only
  character buffer, not int

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if-then-else
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The if statement

• gtgtgt if (seq.startswith("C"))
• ... print "Starts with C"
• ...
• Starts with C
• gtgtgt
• A block is a group of lines of code that belong
  together.
• if (lttest evaluates to truegt)
• ltexecute this block of codegt
• In the Python interpreter, the ellipse indicates
  that you are inside a block.
• Python uses indentation to keep track of blocks.
• You can use any number of spaces to indicate
  blocks, but you must be consistent.
• An unindented or blank line indicates the end of
  a block.

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The if statement

• Try doing an if statement without indentation.
• gtgtgt if (seq.startswith("C"))
• ... print "Starts with C"
• File "ltstdingt", line 2
• print "Starts with C"
• IndentationError expected an indented block

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Multiline blocks

• Try doing an if statement with multiple lines in
  the block.
• gtgtgt if (seq.startswith("C"))
• ... print "Starts with C"
• ... print "All right by me!"
• ...
• Starts with C
• All right by me!

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Multiline blocks

• What happens if you dont use the same number of
  spaces to indent the block?
• gtgtgt if (seq.startswith("C"))
• ... print "Starts with C"
• ... print "All right by me!"
• File "ltstdingt", line 4
• print "All right by me!"
• SyntaxError invalid syntax

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Comparison operators

• Boolean and, or, not
• Numeric lt , gt , , !, ltgt, gt, lt
• String in

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Examples

• seq 'CAGGT'
• gtgtgt if ('C' seq0)
• ... print 'C is first'
• ...
• C is first
• gtgtgt if ('CA' in seq)
• ... print 'CA in', seq
• ...
• CA in CAGGT
• gtgtgt if (('CA' in seq) and ('CG' in seq))
• ... print "Both there!"
• ...
• gtgtgt

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Beware! versus

• Single equal assigns a variable name.
• gtgtgt myString "foo"
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• NameError name 'myString' is not defined
• gtgtgt myString "foo"
• gtgtgt myString "foo"
• True

• Double equal tests for equality.
• gtgtgt if (myString "foo")
• File "ltstdingt", line 1
• if (myString "foo")
• SyntaxError invalid syntax
• gtgtgt if (myString "foo")
• ... print "Yes!"
• ...
• Yes!

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if-else statements

• if lttest1gt
• ltstatementgt
• else
• ltstatementgt
• The else block executes only if lttest1gt is false.
• gtgtgt if (seq.startswith('T'))
• ... print 'T start'
• ... else
• ... print 'starts with', seq0
• ...
• starts with C
• gtgtgt

Evaluates to FALSE no print.
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if-elif-else

• if lttest1gt
• ltstatementgt
• elif lttest2gt
• ltstatementgt
• else
• ltstatementgt
• elif block executes if lttest1gt is false and then
  performs a second lttest2gt

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Example

• gtgtgt base 'C'
• gtgtgt if (base 'A')
• ... print "adenine"
• ... elif (base 'C')
• ... print "cytosine"
• ... elif (base 'G')
• ... print "guanine"
• ... elif (base 'T')
• ... print "thymine"
• ... else
• ... print "Invalid base!
• ...
• cytosine

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• ltfilegt open(ltfilenamegt, rwagt
• ltstringgt ltfilegt.read()
• ltstringgt ltfilegt.readline()
• ltstring listgt ltfilegt.readlines()
• ltfilegt.write(ltstringgt)
• ltfilegt.close()

• if lttest1gt
• ltstatementgt
• elif lttest2gt
• ltstatementgt
• else
• ltstatementgt

• Boolean and, or, not
• Numeric lt , gt , , !, ltgt, gt, lt
• String in, not in

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Sample problem 1

• Write a program read-first-line.py that takes a
  file name from the command line, opens the file,
  reads the first line, and prints the result to
  the screen.
• gt python read-first-line.py hello.txt
• Hello, world!
• gt

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Solution 1

• import sys
• filename sys.argv1
• myFile open(filename, "r")
• firstLine myFile.readline()
• myFile.close()
• print firstLine

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Sample problem 2

• Modify your program to print the first line
  without an extra carriage return.
• gt python read-first-line.py hello.txt
• Hello, world!
• gt

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Solution 2

• import sys
• filename sys.argv1
• myFile open(filename, "r")
• firstLine myFile.readline()
• firstLine firstLine-1
• myFile.close()
• print firstLine

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Sample problem 3

• Write a program add-two-numbers.py that reads one
  integer from the first line of one file and a
  second integer from the first line of a second
  file and then prints their sum.
• gt add-two-numbers.py nine.txt four.txt
• 9 4 13
• gt

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Solution 3

• import sys
• fileOne open(sys.argv1, "r")
• valueOne int(fileOne.readline())
• fileTwo open(sys.argv2, "r")
• valueTwo int(fileTwo.readline())
• print valueOne, "", valueTwo, "", valueOne
  valueTwo

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Sample problem 4

• Write a program find-base.py that takes as input
  a DNA sequence and a nucleotide. The program
  should print the number of times the nucleotide
  occurs in the sequence, or a message saying its
  not there.
• gt python find-base.py A GTAGCTA
• A occurs at position 3
• gt python find-base.py A GTGCT
• A does not occur at all

Hint S.find('G') returns -1 if it can't find
the requested sequence.
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Solution 4

• import sys
• base sys.argv1
• sequence sys.argv2
• position sequence.find(base)
• if (position -1)
• print base, "does not occur at all"
• else
• print base, "occurs at position", position

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Reading

• Chapter 13 of Learning Python (3rd edition) by
  Lutz.