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subsetting data

 
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# 1  
Old 09-01-2008
subsetting data
I have a file where the data is stored in 6 columns, I would like to subset only lines with the fourth column is blank.
Can anybody help me with this?
Thanks
Joseph
# 2  
Old 09-01-2008
Quote:
Originally Posted by jdhahbi
I have a file where the data is stored in 6 columns, I would like to subset only lines with the fourth column is blank.
Can anybody help me with this?
Thanks
Joseph
Provide a sample input and output
# 3  
Old 09-01-2008
input:

infile:
1 B 1 chr5 VF
2 C 2 CF
3 D a CA
4 E c chrM AC

outfile:
2 C 2 CF
3 D a CA
# 4  
Old 09-01-2008
There would be one limitation here..
that system will not identify whether the netry for the 4th column is missing or not, for it will consider the 5th column as 4th..One approch is that if we know that the 4th column length is 4 and fifth column length is 2 (as shown in ur example), it would be easy..

Code:
awk '{ if(length($4)==2) print; }'  filename

# 5  
Old 09-01-2008
I am sorry the formatting did not come out right to reflect what I meant.
here is another trial:

input
Code:
#col1 #col2 #col3 #col4 #col5 #col6
   a        b       c       d       e      f

output
Code:
#col1 #col2 #col3 #col4 #col5 #col6
   a        b       c                e      f

I want data that looks like the second row where col4 is blank
Last edited by radoulov; 09-01-2008 at 03:40 PM.. Reason: added code tags
# 6  
Old 09-01-2008
Hm, could you post a bigger sample from your input using code tags?
Is the field separator a fixed number of spaces?
# 7  
Old 09-01-2008
I hope I got it right this time.
In my real data, the length of both fourth and fifth columns is variable

input
Code:
#col1 #col2 #col3 #col4 #col5 #col6
   a        b       c       d       e      f
   a        b       c                e      f

output
Code:
#col1 #col2 #col3 #col4 #col5 #col6
   a        b       c                e      f

Last edited by radoulov; 09-01-2008 at 03:52 PM.. Reason: added code tags
 
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