Monthly Archives: May 2011

Shell command to print the number of occurrences of chromosomes

  The following is a text file containing human genetics data. 

Here is the command to print the number of 
occurrences of chromosomes from the above data file:
grep -v "^#" 1000gp.vcf| cut -f 1 | sort | uniq -c

Here a pipeline symbol '|' is used to combine 
several commands into a single one. A pipe uses
output of the command on its left side as the
input to its right side.

Now let's see the use of each keyword in the command. 
grep -v "^#" is used to print the lines other than
header files,i.e lines which are not starting with 
"#" from the given file.cut -f 1 is used to select 
only the first field from its input.sort is used to
sort the lines in the ascending order.uniq -c is 
used to print the number of occurrences by omitting 
the repeated value.
Thus the final result will be the list of unique 
chromosomes ,each of with their number of occurrences.


Hi friends,

I am Ramya, doing MCA in GEC Thrissur. I am here to share my ideas about the projects that i am going to do in my course. I am expecting your valuable feedbacks and as a beginner it will help me to improve a lot .

Thank you