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find strings at the start of a particular column

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# 1  
Old 12-09-2010
find strings at the start of a particular column
Hey,

I have not posted here in a while. I have a biological data file that has 4 columns and I am interested in column 2. Column 5 contains a series of letters AGCT.

Basically the file looks something like this

Code:
Name   AGGTTTTCCCCCCC  L  Q
Name1  AGGTTTTAAAAAACC  L  Q
Name2  ATTGGGGGGGGGGG  L  Q

The file is tab delimited and if it column 2 begins with AGG then I want it to go into another file.

Thanks
Kylle
# 2  
Old 12-10-2010
awk ' { if (substr($2,0,3) == "AGG") print $0; } ' data.txt > sorted_data.txt

data.txt contains your regular data sorted_data.txt is the new file with lines that have AGG
Last edited by codecaine; 12-10-2010 at 01:52 AM..
# 3  
Old 12-10-2010
Code:
grep "^IAGG[A-Z]^I" file > newfile            # where ^I represents tab

grep "^.*^IAGG[A-Z]^I.*^I.*$" file > newfile   # for an exact match

R0H0N
# 4  
Old 12-10-2010
could try..
Code:
awk '$2 ~ /^AGG/' inputfile > outfile

This User Gave Thanks to michaelrozar17 For This Post:
codecaine
# 5  
Old 12-10-2010
Quote:
Originally Posted by michaelrozar17
could try..
Code:
awk '$2 ~ /^AGG/' inputfile > outfile

I like this way. Thank you for the share.
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