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Grep -w not printing exact matches

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# 1  
Old 07-07-2015
Grep -w not printing exact matches
Dear All,

Here is my input

Code:
TAACGCACTTGCGGCCCCGGGATAAAAAAAAAAAAAAAAAAAAATGGATT
NAGAGGGACGGCCGGGGGCATAAAAAAAAAAAAAAAAAAAAAGGGATTTC
NGGGTTTTAAGCAGGAGGTGTCAAAAAAAAAAAAAAAAAAAAAGGGATTT
NTGGAACCTGGCGCTAGACCAAAAAAAAAAAAAAAAAAAATGGATTTTTG
ATACTTACCTGGCAGGGGAGATACCATGATCAATAAAAAAAAAAAAAAAA
NACAAAGCATCGCGAAGGCCCGCGGCAAAAAAAAAAAAAAAAAATGGGAT

When I try this command
Code:
cat 1 | grep AAAAAAAAAAAAAAAAAAAAA

I get this output

Code:
TAACGCACTTGCGGCCCCGGGATAAAAAAAAAAAAAAAAAAAAATGGATT
NAGAGGGACGGCCGGGGGCATAAAAAAAAAAAAAAAAAAAAAGGGATTTC
NGGGTTTTAAGCAGGAGGTGTCAAAAAAAAAAAAAAAAAAAAAGGGATTT

But when I try

Code:
cat 1 | grep -w "AAAAAAAAAAAAAAAAAAAAA"

I get nothing in my output. I would like to search for exact strings in a file with more than 6 million lines.

Please comment.
# 2  
Old 07-07-2015
Your first attempt was an exact match already. Every line you got contained the string "AAAAAAAAAAAAAAAAAAAAA".
# 3  
Old 07-07-2015
You get nothing because you're asking for an exact word match i.e. the word "AAAAAAAAAAAAAAAAAAAAA"

Yet, there's no word as such in your example.

Let's say your looking for the word "ULTIMATE" in file 1 in a string like :
AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDDULTIMATEDDDDDDDDDDDDJJJJJJJ

Code:
grep ULTIMATE 1

Will give you the following output :
Code:
AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDDULTIMATEDDDDDDDDDDDDJJJJJJJ

While

Code:
grep -w "ULTIMATE" 1

Will give you nothing as no such word exists...

Then again if you had the following string in file 1 : AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDD ULTIMATE DDDDDDDDDDDDJJJJJJJ

Both
Code:
grep ULTIMATE 1

and
Code:
grep -w "ULTIMATE" 1

would give you the same output, that is :

Code:
AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDD ULTIMATE DDDDDDDDDDDDJJJJJJJ

Last edited by vincent72; 07-07-2015 at 07:20 PM..
# 4  
Old 07-08-2015
You probably want
Code:
grep "[^A]AAAAAAAAAAAAAAAAAAAAA[^A]" 1

?
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