CODEWITHSUNDEEP
regexbashpattern-matching
mbk0asis
mbk0asis

Reputation: 99

Bash - count a pattern and print the line containing the pattern

everyone! While I was reading this discussion, "Count number of occurrences of a pattern in a file (even on same line)", I wondered if I could add the line containing the pattern next to the count values.

Somehow I wasn't able to add any comment on the discussion, so I'm posting a new question. Can somebody en-light me?

There must be some misunderstanding here, so I put an example. Let's say, I have a DNA sequence like below and want to find out how many 'CG' are present in each line. 

ACAAAGAACTCAAGAAGTTGGACCCCAGAGAACCAAATAACCCTATTAAA
AATTCGGAACAGAGATAAACAAAGAATTCTCAACTGAGGAAACTTGAATG
GGATTTTTTTTTAAGATTCACTTATTTTTATTTTCTGCATGAGTGTTTGC
CTCGATGTATGTACATATACGACATGTGTACGTGGTGCGCAAGTAAGCAG

Additionally, I want to print each line (not the pattern) along with the pattern counts.

0 ACAAAGAACTCAAGAAGTTGGACCCCAGAGAACCAAATAACCCTATTAAA
1 AATTCGGAACAGAGATAAACAAAGAATTCTCAACTGAGGAAACTTGAATG
0 GGATTTTTTTTTAAGATTCACTTATTTTTATTTTCTGCATGAGTGTTTGC
4 CTCGATGTATGTACATATACGACATGTGTACGTGGTGCGCAAGTAAGCAG

I wish the example above will help to understand the question better.

Thank you!

Upvotes: 0

Views: 409

Answers (3)

mbk0asis
mbk0asis

Reputation: 99

I just found a really simple and elegant solution using EXCEL. The formula goes like below...

=(LEN(B2)-LEN(SUBSTITUTE(B2,"CG","")))/2

What this formula basically does is it counts total length of strings in a cell and length after removal of the pattern ("CG" in this case), then subtract them. Since each "CG" is replaced by blanks, 2 strings are missing after substitution, and you can get the number of the pattern by dividing it with length of your pattern which is 2 in this case.

For example, following sequence contains 50 strings and 13 CG's.

CAGTGCACACAACACATGTACGCGCGCGCGCGCGCGCGCGCGCGCGTGTG  50

After substituting "CG" to blanks, you get 24 strings.

CAGTGCACACAACACATGTATGTG  24

To count the "CG" occurances, 

(50-24)/2 = 13

If you are looking for "CAG", enter "CAG" instead of "CG" and divide by 3. How simple is that!

You can see the original post in the following link.

http://fiveminutelessons.com/learn-microsoft-excel/count-occurrences-single-character-cell-excel#sthash.H4VfOkGB.dpbs

English is not my primary language, so please understand errors in my writing.

People are geniuses!

Upvotes: 0

Anirudha
Anirudha

Reputation: 32787

cat fileName | grep pattern | uniq -c

Upvotes: 1

heemayl
heemayl

Reputation: 41987

You can do:

printf 'pattern' | tee >(sed 's/$/ : /') | grep -cf - input.txt

Taking help of tee and process substitution.

Example:

% cat file.txt 
foobar
spamegg
foo

% printf 'foo' | tee >(sed 's/$/ : /') | grep -cf - file.txt 
foo : 2

Upvotes: 1

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