grep

grep (globally search a regular expression and print) is one of the most useful commands in UNIX and it is commonly used to filter a file/input, line by line, against a pattern eg., to print each line of a file which contains a match for pattern.

grep PATTERN FILENAME

Like any other command there are various options available for this command. Most useful options include:

With options, syntax is

grep [OPTIONS] PATTERN FILENAME

Some typical scenarios to use grep:

• Counting number of sequences in a multi-fasta sequence file
• Get the header lines of fasta sequence file
• Find a matching motif in a sequence file
• Find restriction sites in sequence(s)
• Get all the Gene IDs from a multi-fasta sequence files and many more.

Now let's use grep command to do some simple jobs with the sequences:

1. Counting sequences:

By FASTA format definition, we know that number of sequences in a file should be equal to the number of description lines. So by counting > in file, you can count the number of sequences. This can be done using counting option of the grep with its count option -c.

grep -c ">" FILENAME

However, note that if the deflines somehow have > more than once, it will mess up the count! to be safe, you can use:

grep -c "^>" FILENAME

Task 2.3: Count the number of sequences AT_cDNA.fa and RefSeq.faa

grep -c ">" AT_cDNA.fa
grep -c ">" RefSeq.faa

2. Looking for genes or features:

If you are looking for information about the sequences, you can list all the headers (description lines) for the sequences using grep. Simply search for > and grep will list all the description lines.

grep ">" FILENAME
grep ">" AT_cDNA.fa

Alternatively, you can send it to a file if you want to use it later or you can just pipe it to less or more command to scroll through it line by line or page by page.

grep ">" FILENAME > HEADERFILE.txt
grep ">" FILENAME | less
grep ">" AT_cDNA.fa | less		

Use ↑ or ↓ arrow keys to move up and down, press q to exit

3. Subtracting one list from another:

If there is a small list of genes that you want to remove from a larger list, you can use the grep function with these options:

grep -Fvw -f sub_list.txt full_list.txt

here -F and -w will make sure that the full word is used as literal string, -v will NOT print the matching patterns and -f filename.txt is to say that the input patterns are in the file.

4. Count a word:

Unlike previous example, if the word your are searching occurs more than once in a line, it will only be counted once. To avoid this, you need to use a special option

grep -o "PATTERN" FILENAME

Now, all sorts of useful information can be obtained by just printing the pattern, instead of entire line. For example, how many times do you see a word in every line:

grep -on "PATTERN" FILENAME | cut -f 1 -d ":" | sort | uniq -c

This will print line number followed by number of times you see the PATTERN in that line.

Now, let us have some fun with grep! See what kind of sequences are in AT_cDNA.fa file. Do they all seem to belong to same organism? Which organism?

Using grep you can also locate all the lines that contain a specific term you are looking for. This is very useful, especially to look for a specific gene among a large number of annotated sequences.

grep "word or phrase to search" FILENAME

Task 2.4: Try searching for your favorite gene, to see if it is present in AT_cDNA.fa (this file contains all annotated sequences for Arabidopsis thaliana). Unlike Google or any search engines, only exact search terms will be identified, but you can ask grep to ignore cases while searching using -i option. Try these:

grep -i "transcription factor" AT_cDNA.fa
grep -i "TFIIIA" AT_cDNA.fa

You can also use this feature to see if your sequence of interest has a specific feature (restriction site, motif etc.,) or not. This can be performed better using --color option of the grep.

5. Search a motif:

Go to the sequences directory, search for EcoR1 (GAATTC) site in the NT21.fa file, and use the color option. Also, try looking for a C2H2 zinc finger motif in RefSeq.faa file (for simplicity let's assume zinc finger motif to be CXXXCXXXXXXXXXXHXXXH. Either you can use dots to represent any amino acids or use complex regular expressions to come up with a more representative pattern. Try these:

grep --color "GAATTC" ./Sequences/NT21.fa
grep --color "C..C............H...H" RefSeq.faa

6. Finding patterns that DOES NOT match:

You can also use grep command to exclude the results containing your search term. Say if you want to look at genes that are not located in chromosome 1, you can exclude it form your search by specifying -v option.

grep -i "transcription factor" AT_cDNA.fa| grep -v "chr1"
grep -i "transcription factor" AT_cDNA.fa| grep "chr1"

Notice the difference in output from the above two commands.

7. Searching for more than one pattern:

You can also use grep to find as set of patterns in the same command. grep will print the line containing any one of those patterns you specify. For this, run it as follows:

Any one pattern of the three (OR)

grep 'pattern1|pattern2|pattern3' FILENAME

All three patterns (AND)

grep 'pattern1' FILENAME | grep 'pattern2' | grep 'pattern3'

Note that in the OR example, | stands for or while in the AND example it pipes the output from one command to another.

Try to understand the following command lines (and record your results, where applicable):

grep -c -w "ATP" RefSeq.faa
grep -c CGT[CA]GTG AT_cDNA.fa
grep -l "ATG" ./sequences/*.fa

You can also try some regular expressions related to nucleotide/protein sequences provided earlier to see how it works.

8. Finding blank lines

grep can also be used to find blank lines. From the regex above, you have seen that ^ marks the beginning of a line, while $ marks the end. So, by searching for ^$ you are looking for lines that have no content (blank).

grep "^$" FILENAME

Similarly, if you want to remove blank lines, you can try:

grep -v "^$" FILENAME

9. Finding all the files that contain a term

When dealing with multiple files, you will end up in situations where you want to process subset of files that are of interest. To quickly find those file, knowing a unique term that occurs in them, you can use grep

grep -rl "PATTERN" .

here -r recursively searches all files in sub-folders and -l, rather than printing the matching line, prints the filename after the first occurrence. Note the . at the end, it tells grep to use all the files that are in the directory. The result is that you will have a subset of files that are of interest to you.

If you want files that do not you the term, you can replace -l with -L (like the option -v for negative match). This will list only files that DO NOT have any match.

grep -rL "PATTERN" .

10. Print lines before or after the matching term

With the regular grep search, you get the line containing the matching term. Sometimes, in order to know the context of this term, it is useful to print either lines before or after the term occurrence. With -B (for before) and -A (for after), you can specify the number of lines that you want to see.

grep -B 10 "PATTERN" FILENAME

This will print 10 lines (including the line that has the PATTERN) before the match

Similarly, to print lines after the match:

grep -A 10 "PATTERN" FILENAME

You can also combine to get both before and after lines

grep -B 10 -A 10 "PATTERN" FILENAME

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