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Delete column with exact string in specific col

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# 1  
Old 06-28-2013
Delete column with exact string in specific col
Hi,
my file structur looks like
Code:
File structure looks:
GeneID protein_gi Symbol
1246500 10954455 repA1
1246501 10954457 repA2
1246502 10954458 leuA

But some of the cases do not have record for protein id. for example:
Code:
1343044 - orf01

I want to remove those rows.

But I tried
Code:
awk -F, '$2==!/-/' file.txt >test1.txt 
awk -F' ', '$2==!/-/' file.txt >test1.txt

None of them are working.
Can anybody please help? Thanks a lot,Mitra

---------- Post updated at 06:51 AM ---------- Previous update was at 06:48 AM ----------

I also tried
Code:
awk -F' ', '$2=='-'' file.txt >test1.txt

But got error like
Code:
awk: syntax error at source line 1
 context is
	 >>>  <<< 
awk: bailing out at source line 1

Last edited by smitra; 06-28-2013 at 02:51 AM.. Reason: typo error
# 2  
Old 06-28-2013
try this

Code:
awk '{if ($2!="-") print}' file.txt

or


Code:
awk '$2!="-" {print} ' file.txt

Last edited by krishmaths; 06-28-2013 at 03:03 AM.. Reason: Added alternative solution
This User Gave Thanks to krishmaths For This Post:
smitra
# 3  
Old 06-28-2013
Is your file comma seperated? if space seperated..

Code:
 
awk '$2 ~ !/-/{print $0}' filename

This User Gave Thanks to vidyadhar85 For This Post:
smitra
# 4  
Old 06-28-2013
Code:
grep -v "\-" file

These 2 Users Gave Thanks to Just Ice For This Post:
RavinderSingh13 smitra
# 5  
Old 06-28-2013
Thanks a lot all for your help. It worked perfectly with krishmath and vidyadhar85's suggestions...
Just Ice, thanks to you also, but as I have "-" in 3rd Gene symbol col also sometimes, thus I prefer to use column number.
Thanks a lot to all again. Smilie

---------- Post updated at 07:38 AM ---------- Previous update was at 07:20 AM ----------

Hello all,
Can anybody suggest me why the new file sizes created by all above commands differ? only first two are identical with awk...
Code:
awk '{if ($2!="-") print}' file.txt

or
Code:
awk '$2!="-" {print} ' file.txt

But with
Code:
awk '$2 ~ !/-/{print $0}' filename

and
Code:
grep -v "\-" file

provide different file size... I am comparing as my input file is same, and for this occasion I have no '-' in other cols.

Any suggestion whould be good.
Thanks,
Mitra
# 6  
Old 06-28-2013
Quote:
Originally Posted by smitra
Thanks a lot all for your help. It worked perfectly with krishmath and vidyadhar85's suggestions...
Just Ice, thanks to you also, but as I have "-" in 3rd Gene symbol col also sometimes, thus I prefer to use column number.
Thanks a lot to all again. Smilie

---------- Post updated at 07:38 AM ---------- Previous update was at 07:20 AM ----------

Hello all,
Can anybody suggest me why the new file sizes created by all above commands differ? only first two are identical with awk...
Code:
awk '{if ($2!="-") print}' file.txt

or
Code:
awk '$2!="-" {print} ' file.txt

But with
Code:
awk '$2 ~ !/-/{print $0}' filename

and
Code:
grep -v "\-" file

provide different file size... I am comparing as my input file is same, and for this occasion I have no '-' in other cols.

Any suggestion whould be good.
Thanks,
Mitra
I guess the below command stops printing after it encounters a "-" in 2nd column.
Code:
awk '$2 ~ !/-/{print $0}' filename

The
Code:
grep -v

should work fine. Are you sure you don't have any other "-" in the file?
This User Gave Thanks to krishmaths For This Post:
smitra
# 7  
Old 06-28-2013
Thanks krishmaths,
Yes I guess that is the case. As first two commands deliver the file with size >300MB
But other just over 200MB.

No I am not sure..in some cases files may have - in other cols...thus I also prefer $2!="-"
Thanks for explaining.
Mitra.
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