Day-1 Day-2 Day-3 Day-4 Day-5 Day-6 Day-7 Day-8

Linux

List of linux commands

So far…

S.No.	Command	Function
1.	mkdir	make a new directory
2.	rmdir	remove an empty directory
3.	touch	create a new file
4.	rm	remove a file
5.	cp	copy a file
6.	mv	move/rename a file
7.	ls	list the contents of a directory
8.	pwd	present working directory
9.	cd	change directory
10.	ssh	Secure Shell - helps gain access to a remote server via secure channel
11.	echo	Equivalent of print() function in python
12.	head	Displays the first 10 lines of a file
13.	tail	Displays the last 10 lines of a file
14.	cat	Displays the entire contents of a file
15.	scp	Secure Copy - helps to copy/transfer files between host and server
16.	>	Redirection Operator
17.	chmod	Change Mode - used to change file permissions

Shortcuts with cd

S.No.	Symbol	Description
1.	.	This directory/ Present directory (Period)
2.	..	One directory up the hierarchy (Double Dot)
3.	-	Previous location (Hyphen)
4.	~	Home (Tilde)

This week

S.No.	Command	Function
18.	grep	Matches pattern and returns the matching lines/number of lines/non matching lines.
19.	awk	Pattern searching and processing language. Powerful as a complete language.
20.	sed	Basic text transformation on a input line or file.

General usage of grep, awk and sed:

grep "pattern" filename
awk '{function}' filename
sed 's/word.to.replace/replacing.word/' filename

Some options with grep

S.No.	Option	Description
1.	n	line number
2.	v	All others except search pattern (Negation)
3.	c	Count the number of lines with matching pattern
4.	l	File name of the matching files
5.	i	Case insensitive
6.	x	Exact matches only
7.	E	Used to search for regular Expressions

Some options with awk

S.No.	Option	Description
1.	F	(Input) Field separator
2.	OFS	Output Field Separator
3.	$0	All columns

awk '{print $1,$2,$3}' file.txt
ls -l| awk 'BEGIN {sum=0} {sum=sum+$5} END {print sum}'

Some options with sed

S.No.	Option	Description
1.	e	match pattern
2.	n	line number
3.	i	Case insensitive

Frequently Used flag in sed is g in the expression

sed -ei 's/U/X/g' protein-sequence.txt

Challenge

1. Extract protein product and description in the following tab-separated(tab) file into a comma-separated (csv) file.
2. A software that calls for bases while sequencing had a bug which made all the Adenine in the sequence marked as “X” instead of “A”. You called the customer support and they fixed the bug by releasing a new update to the software. But your lab had insufficient fund to update to the newer version. You inform your PI and he tells you to write a script to fix this issue in your sequence. How will you fix this? (You can not update the software using personal funds)
3. Search the following 8 nucleotide sequence in this file: “tagctgatc”. Report the lines in which they occur.

Python

So far we have seen Data types (int, str, float), Data Structures (list and dictionary) and Condition statements (if, elif and else). Today we will see tuples which is another data structure and looping (for and while loops) in python.

Tuples

Tuples are similar to lists. They can hold different data types and structures. All the elements in the tuples are indexed like list. But a crucial difference between a tuple and a list is that the tuples are immutable. This feature makes tuple an asset when dealing with nucleotide and protein sequences.

General Usage:

Assigning a tuple to a variable

tuple = ()

Example of a tuple

tuple = ("ATGCATGCAGCATC", "RHGLYHGRYLYCHRGL", ["DNA","RNA",4], 576)

Challenge:

Extract “RNA” from the tuple above.

Loops

Loops are of immense help when it comes to doing a repetitive work for an entire file/ sometimes directory. We can iterate using two loops. They are for loop and while loop.

while loop

The while loop repeats a block of commands/instructions as long as a given condition is True. Each repetition is called an iteration of the loop.

n = 1

while n < 4:
	print(n)
	n = n + 1

num = 1

while num <= 10:
    print(num)
    num += 1

General Syntax:

loop_condition = True

while loop_condition:
    print("Loop Condition keeps: %s" %(loop_condition))
    loop_condition = False

for loop

The for loop is another way to iterate over a list or a file or over a range of values. A for loop automatically assigns a variable to the current element being iterated on.

for i in range(1, 11):
  print(i)

In the code above, the variable i is a placeholder for the element currently being iterated on.

with open as

To open a file, the function open() is used. This function takes two arguments. The first argument is the name or the path to the file. The second argument specifies a mode in which the file should be opened.

There are three modes.

r - read w - write a - append

So the general syntax is

with open ("DNA.sequence.file.fasta", 'r') as infile:
  for line in infile:
    print line

Challenge

1. Given two numbers a and b. Find the sum of all odd numbers between the two.
2. Given a file, print only the even numbered lines from the file. Assume 1-based numbering of lines.
3. Given a string, count the number of times each word appears.