How to use the programming in UNIX to count the total G+C and the GC%?What command li


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting How to use the programming in UNIX to count the total G+C and the GC%?What command li
# 1  
Old 01-20-2009
How to use the programming in UNIX to count the total G+C and the GC%?What command li

Seems like can use awk and perl command. But I don't have the idea to write the command line. Thanks for all of your advise.
For example, if I have the file whose content are:
Sample 1. ATAGCAGAGGGAGTGAAGAGGTGGTGGGAGGGAGCT
Sample 2. ACTTTTATTTGAATGTAATATTTGGGACAATTATTC
Sample 3. AAATCATGGTGGGTTTATTGATGGTTAGAAAGTTCC
All the sample above, got 36 nucleotide.

I want my output to count the G + C and GC %. So my output should look like this:
Sample 1: G+C = 21 GC%= 58.33%
Sample 2: G+C = 8 GC%=22.22%
Sample 3: G+C = 13 GC%=36.11%

Thanks and appreciate of your answer.
# 2  
Old 01-20-2009
No duplicate or cross-posting, please read the rules.

Continue here:

https://www.unix.com/shell-programmin...#post302278286


Thread closed.
Login or Register to Ask a Question

Previous Thread | Next Thread

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Finding total distinct count from multiple csv files through UNIX script

Hi All , I have multiple pipe delimited csv files are present in a directory.I need to find out distinct count on a column on those files and need the total distinct count on all files. We can't merge all the files here as file size are huge in millions.I have tried in below way for each... (9 Replies)
Discussion started by: STCET22
9 Replies

2. Shell Programming and Scripting

Count total duplicates

Hi all, I have found another post threads talking about count duplicate lines, but I am interested in obtain the total number of duplicates. For example: #file.txt a1 a2 a1 a3 a1 a2 a4 a5 #out 3 (lines are duplicates) Thank you! (12 Replies)
Discussion started by: mikloz
12 Replies

3. UNIX for Dummies Questions & Answers

Count total image in directory

Dear all, I have a directory consisted of files in .jpg, .jpeg etc..all of them are image 20140411030143_62811159403_92886.jpg 5/11/2014 15:01 197K 20140415024737_62811618747_116460.jpg 4/15/2014 14:47 17K 20140415031003_62811618747_109192.jpg 4/17/2014 15:10 17K... (4 Replies)
Discussion started by: radius
4 Replies

4. UNIX for Dummies Questions & Answers

In ls -l remove total count

Hi All, When i give ls -ltr i get 'total 10' like this along with files long listing. is there any option in ls command to remove this line or do we need use head -1 command only. $ls -ltr total 45 -rw-r--r-- 1 abc g1 0 Jul 17 07:20 0 -rw-r--r-- 1 abc g1 744 May 9 12:10 a -rw-r--r--... (1 Reply)
Discussion started by: HemaV
1 Replies

5. Shell Programming and Scripting

Total Count using AWK

Hi Everybody, I have the following example file... 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1 199|TST-GURGAON|GURGAON|1... (8 Replies)
Discussion started by: sraj142
8 Replies

6. UNIX for Dummies Questions & Answers

How does unix system administration, unix programming, unix network programming differ?

How does unix system administration, unix programming, unix network programming differ? Please help. (0 Replies)
Discussion started by: thulasidharan2k
0 Replies

7. Shell Programming and Scripting

Bogus Total count

I have a shell script that I am pulling different zip file packages and totaling how many of each type of package is in the directory. I get a bogus total count of one in the middle of my output file (highlighted in RED) and not sure why, also would like to get a grand total of all files but not... (2 Replies)
Discussion started by: freddie999
2 Replies

8. Shell Programming and Scripting

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:... (2 Replies)
Discussion started by: patrick chia
2 Replies

9. UNIX for Advanced & Expert Users

total count of inodes in a mount

is there Any command to get total count and number of free inodes on a mount. please help (5 Replies)
Discussion started by: pharos467
5 Replies
Login or Register to Ask a Question