Uppercase/lowercase comparison of one character per line with awk??

Login or Register to Ask a Question and Join Our Community

Uppercase/lowercase comparison of one character per line with awk??

Tags

Top Forums Shell Programming and Scripting Uppercase/lowercase comparison of one character per line with awk??

Prev Next

01-07-2010

Registered User

28, 0

Join Date: Dec 2009

Last Activity: 1 September 2014, 1:07 PM EDT

Posts: 28

Thanks Given: 1

Thanked 0 Times in 0 Posts

Uppercase/lowercase comparison of one character per line with awk??

Another frustrating scripting problem from a biologist trying to manipulate a file with several millions line. For each of the line I need to compare the uppercase A or C or G or T with the lowercase a or c or g or t. If there are more uppercases, a + should be added to a new column, otherwise a - is added. Many of the lines are duplicated or even triplicated, etc... This is to allow the comparison of only one character at a time in the order of ACGT. And to make it even more complicated, comparison on the last line of the repeated lines should be between the . and , where if there are more . than , a + should be added.

Below are the examples of some of my data. The columns with numbers are the count of uppercase ACGT and lowercase acgt respectively.

Code:

.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0

And this is what I'll like to get:

Code:

.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  +
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  -
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  +

I've tried awk with if conditions but I guess it is too simple. Any suggestions or help will be very much appreciated!

Last edited by Scott; 01-07-2010 at 02:38 AM.. Reason: Added code tags

ivpz

View Public Profile for ivpz

Find all posts by ivpz

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Uppercase to lowercase

Hello, I have a list of files in a directory whose names are all in uppercasse, including the file format for eg *.MP3 . I would like to convert these to the normal way we write it ie ABC.MP3 to be converted to Abc.mp3 . I know that this can be done manually by using a lot of "mv" or rename...

2. Shell Programming and Scripting

Convert lowercase to uppercase

listprocs.sh contains ps -ef | grep "swikar" 1) Write a shell script to convert an input file to all upper case. Name your shell script toupper.sh. Hint: tr ' ' ' ' will convert all lower case letters to upper case To use your script, try the following command: cat...

3. UNIX for Dummies Questions & Answers

UPPERCASE to lowercase

Hi All, i have a file and i want to convert all uppercase letters to lowercase letters which are in my file. how can i do this. Thanx

4. UNIX Desktop Questions & Answers

Unix: lowercase to uppercase

I just started to learn unix... and i needed to make a basic script. i need to 1. read a file (.txt) 2. count the words of EVERY sentece 3. sentences with odd number of words need to be converted into lowercase sentences with even number of words need to be converted into uppercase ...

5. Shell Programming and Scripting

indentation and lowercase to uppercase

hi, i need to write a bash script that does two things. the program will take from the command line a file name, which is a C code, and an integer, which is the size of my indentation i would then have to indent every nested code by the number of columns provided by the user in the...

6. UNIX for Dummies Questions & Answers

uppercase to lowercase

i have no variable and no file i just want to convert AJIT to ajit with some command in UNIX can anybody help

7. AIX

Lowercase to Uppercase

Inside a script I have 2 variables COMP=cy and PT=t. further down the same script I require at the same line to call those 2 variables the first time uppercase and after lowercase ${COMP}${PT}ACE,${COMP}${PT}ace. Can somebody help me Thanks in advance George Govotsis

8. Shell Programming and Scripting

UPPERCASE to lowercase with no overwriting?

Hey, I've just started learning shell script today. How would I write a bash script file that changes file names from uppercase to lowercase in that directory, the program should warn the user and NOT overwrite the existing file if it's already in lowercase? for example in a directory i...

9. Shell Programming and Scripting

How convert lowercase or uppercase

It will only accept one argument where it should be upper or lowercase. if user choose to convert filnames to upper case than it should convert to upper or vice versa. if no action taken by the user then should not do anything any of the files in the current directory.

10. Shell Programming and Scripting

uppercase to lowercase

Greetings & Happy New Years To All! A client of mine FTP'ed their files up to the server and it all ended up being in UPPERCASE when it all should be in lowercase. Is there a builtin command or a script anyone knows of that will automagically convert all files to lowercase? Please advise asap...

Login or Register to Ask a Question