Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

How can I calculate the total of nucleotide in Unix?What command line I should type?

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting How can I calculate the total of nucleotide in Unix?What command line I should type?
# 1  
Old 01-22-2009
How can I calculate the total of nucleotide in Unix?What command line I should type?
For example, if I have the file whose content are:
>HWI-EAS382_30FC7AAXX:7:1:927:1368
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:7:1:924:1373
ACGAACTTTAAAGCACCTCTTGGCTCGTATGCCGTC

I want my output calculate the total of nucleotide. So my output should look like this:
>HWI-EAS382_30FC7AAXX:7:1:927:1368
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36
>HWI-EAS382_30FC7AAXX:7:1:924:1373
ACGAACTTTAAAGCACCTCTTGGCTCGTATGCCGTC 36
# 2  
Old 01-22-2009
If thats all you need to do then maybe a shell script is the way to go, but if you want a single interface to all your DNA needs you might want to look into BioPerl.

Main Page - BioPerl
# 3  
Old 01-22-2009
Code:
awk '!/^>/ {print $0,length($0); next} {print}' infile
>HWI-EAS382_30FC7AAXX:7:1:927:1368
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36
>HWI-EAS382_30FC7AAXX:7:1:924:1373
ACGAACTTTAAAGCACCTCTTGGCTCGTATGCCGTC 36

Login or Register to Ask a Question

Previous Thread | Next Thread

3 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Calculate the total

Hi All , I have the following script as below , I tried to modify to meet the requirement , could someone help ? very thanks ================================================================================================ while read STR NAME; do Total=0 MyString="$STR" GetData () {... (18 Replies)
Discussion started by: ust3
18 Replies

2. Shell Programming and Scripting

Calculate total space, total used space and total free space in filesystem names matching keyword

Good afternoon! Im new at scripting and Im trying to write a script to calculate total space, total used space and total free space in filesystem names matching a keyword (in this one we will use keyword virginia). Please dont be mean or harsh, like I said Im new and trying my best. Scripting... (4 Replies)
Discussion started by: bigben1220
4 Replies

3. Shell Programming and Scripting

How can I remove those duplicate sequence in UNIX?What command line I should type?

The input is: >HWI-EAS382_30FC7AAXX:4:1:1580:1465 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >HWI-EAS382_30FC7AAXX:4:1:1062:1640 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >HWI-EAS382_30FC7AAXX:4:1:272:629 AAAAAAAAGCTATAGTCTCGTCACACATACTCACAA >HWI-EAS382_30FC7AAXX:4:1:1033:1135... (4 Replies)
Discussion started by: patrick chia
4 Replies
Login or Register to Ask a Question