Grep -w not printing exact matches

Shell Programming and Scripting
1

Dear All,

Here is my input

TAACGCACTTGCGGCCCCGGGATAAAAAAAAAAAAAAAAAAAAATGGATT
NAGAGGGACGGCCGGGGGCATAAAAAAAAAAAAAAAAAAAAAGGGATTTC
NGGGTTTTAAGCAGGAGGTGTCAAAAAAAAAAAAAAAAAAAAAGGGATTT
NTGGAACCTGGCGCTAGACCAAAAAAAAAAAAAAAAAAAATGGATTTTTG
ATACTTACCTGGCAGGGGAGATACCATGATCAATAAAAAAAAAAAAAAAA
NACAAAGCATCGCGAAGGCCCGCGGCAAAAAAAAAAAAAAAAAATGGGAT

When I try this command

cat 1 | grep AAAAAAAAAAAAAAAAAAAAA

I get this output

TAACGCACTTGCGGCCCCGGGATAAAAAAAAAAAAAAAAAAAAATGGATT
NAGAGGGACGGCCGGGGGCATAAAAAAAAAAAAAAAAAAAAAGGGATTTC
NGGGTTTTAAGCAGGAGGTGTCAAAAAAAAAAAAAAAAAAAAAGGGATTT

But when I try

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

Your first attempt was an exact match already. Every line you got contained the string "AAAAAAAAAAAAAAAAAAAAA".

3

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

grep ULTIMATE 1

Will give you the following output :

AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDDULTIMATEDDDDDDDDDDDDJJJJJJJ

While

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

grep ULTIMATE 1

and

grep -w "ULTIMATE" 1

would give you the same output, that is :

AAAAAAAAAAJJJJJJJJJJJJJDDDDDDDDDDD ULTIMATE DDDDDDDDDDDDJJJJJJJ
4

You probably want

grep "[^A]AAAAAAAAAAAAAAAAAAAAA[^A]" 1

?