Day_4B.ipynb

Kernel: Python 2

File handling – exercise

• Lets write a (new) file

• Use as a name of the file: "file.txt"

• By using "w" it will overwrite any existing files

• The file will be located in the current working directory, unless you specify the entire path before the filename

# Open a file
file = open("file.txt", "w")
print "Name of the file: ", file.name

File handling – good practice

• After opening also close your files:

• The close() method of a file object flushes any unwritten information and closes the file object, after which no more writing can be done. It is a good practice to use close().

# Open a file
file = open("file.txt", "w")
# do stuff
file.close()

File handling – good practice

• Before opening a file its also good to actually check the file exists

import sys ## module System-specific parameters and functions
try:
    file = open("file.txt", "r")
    # do stuff
    file.close()
except:
    sys.exit("File does not exist!")

File handling – writing

• To write to a file you use the command below:

  • file.write("What you want to write")

• Try yourself to write some variables to a file

file = open("file.txt", "w")

file.write("Hello script!\n") ## write directly

line = "This is my output!"
file.write(line+"\n") ## write string

file.close()

File handling – reading

• Try to read the lines you just wrote to a file in the previous exercise

# Most frequently a file is being read line by line using a loop. 
# This method also reads a file line by line just like readline()
# Example:

file = open("file.txt", "r")
for line in file:
    print line,
file.close()

Newline characters

• Most of the times the newline characters at the end of a line are simply said “annoying”, we can remove them using the following command:

line.rstrip() ## removes newline character

File handling – splitting the lines

• To split your line, you can use the line.split() function using any delimiter (example below)

• But of course if we want to split on a bit more difficult pattern we rather use the Regex split function we discussed this morning

file = open("file.txt", "r")
for line in file:
    splitline = line.split()## you can use different (deliminators)!
    print splitline
file.close()

File handling – exercise

• The file "exercise.bed" contains genomic regions and is rather large, the perfect opportunity to use Python to process this file

• Read the BED file and make an output file were "chr" in front of the number is removed (e.g. chr1 will be 1).

• Determine the number of regions covered in each chromosome (e.g. each line is a region chromosome 1 --> 71906 regions)

• Parse and print to screen the total number of regions and size covered for each chromosome

• Challenge: combine number 1 and 2

# Type here your code

As frequently requested two examples:

• Limit the raw_input to only nucleotides:

import re
input_str = ""
while not re.match("^[actg]{1,}$", input_str,re.I):
    input_str = raw_input("Please provide some nucleotides:")
print input_str

As frequently requested two examples:¶

• make reverse complement a sequence easy:

from string import maketrans
dna_code = "aCGttgagatcagat"
complement = maketrans("acgtACGT", "tgcaTGCA")
print "dna_code:           ", dna_code
print "complement:         ", dna_code.translate(complement)
print "reverse complement: ", dna_code.translate(complement)[::-1]