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Linux

List of linux commands and its function

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

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
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

General format for chmod:

chmod u+x name_of_the_python_file

General format for scp: from host to remote server

scp name_of_the_file username@servername:path/to/the/file

Example:
The following command copies dna.fasta file from present working directory to DNA directory under Documents in the server.

scp dna.fasta manager@pine64.uta.edu:~/Documents/DNA/

General format for scp: from remote server to the host.

scp username@servername:path/to/the/file path/to/where/you/want/to/copy/

Example:
The following command copies dna.fasta from server to present working directory.

scp manager@pine64.uta.edu:~/Documents/DNA/dna.fasta ./

Here is a sample file for your challenge.

Linux Challenge

1. Rename a file without affecting the contents of the file using the command(s) learnt so far.
2. Copy the renamed file from your system to the server using scp command.
3. Print the first 16 lines of the renamed file opening it from the server.
4. Write these 16 lines to results.txt.
5. Copy it from server to your local system.

Python

Last week we discussed lists and dictionaries in python. We also learnt about position and indexing in lists and strings.

Remember:

• Strings are immutable in python whereas lists are mutable.

What does this mean?

Lets try the following example.

subjects = ["Biology", "Physics", "Chemistry", 4, 5, 6]
name = "Dinosaur"

What is the data type of subjects and name ?
Try the following commands and explain what you see.

subjects[3] = "Statistics"
name[3] = "a"

Condition statements

Condition statements are if and else statements. To test multiple conditions, if, elif and else are used. Depending on the number of conditions the number of elif statements can be increased in the program.

Observe the Syntax for if and else statements

a = 5
b = 7
if a < b:
  print(a,"is smaller than",b)
else:
  print(a,"is greater than",b)

For if, elif and else

a = 5
b = 7
if a < b:
  print(a,"is smaller than",b)
elif a == b:
  print(a,"is equal to", b)
else:
  print (a,"is greater than",b)

Comparision operators

S.No.	Operator	Function
1.	>	Greater than
2.	>=	Greater than or equal to
3.	<	Lesser than
4.	<=	Lesser than or equal to
5.	==	Equal to
6.	!=	Not Equal to

Membership operators

S.No.	Operator	Function
1.	in	True if it finds a variable in the specified sequence and false otherwise.
2.	not in	True if it does not finds a variable in the specified sequence and false otherwise.

For example:

dna=input('Enter DNA sequence:')
if "n" in dna :
   nbases=dna.count("n")
   print("dna sequence has %d undefined bases " % nbases)
else:
   print("dna sequence has no undefined bases")

Logical Operators

S.No.	Operator	Function
1.	and	True if both conditions are true
2.	or	True if at least one condition is true
3.	not	True if condition is false

dna=input('Enter DNA sequence:')
if "n" in dna :
   print("dna sequence has undefined bases ")
elif "N" in dna :
   print("dna sequence has undefined bases ")
else:
   print("dna sequence has no undefined bases")

Now using logical operator

dna=input('Enter DNA sequence:')
if "n" in dna or "N" in dna:
   nbases=dna.count("n")+dna.count("N")
   print("dna sequence has %d undefined bases " % nbases)
else:
   print("dna sequence has no undefined bases")

Challenge

1. Find the GC content of a given nucleotide sequence. If GC content is between 40% - 60% display “Suitable candidate for primer”.

2. Create a BMI calculator. Obtain the user’s height and weight. Calculate the BMI and inform the user of his BMI category.