Monthly Archives: May 2011

Shell command to print the number of occurrences of chromosomes

  The following is a text file containing human genetics data.

http://svn.software-carpentry.org/swc/data/1000gp.vcf 

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.
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Ramya

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