CODEWITHSUNDEEP
bashunixgrepmultiline
user3375672
user3375672

Reputation: 3768

grep (bash) multi-line pattern

In bash (4.3.46(1)) I have some multi-line so called fasta records where each record is initiated by on line with >name and the following lines DNA sequence ([AGCTNacgtn]), here three records:

>chr1
AGCTACTTTT
AGGGNGGTNN
>chr2
TTGNACACCC
TGGGGGAGTA
>chr3
TGACGTGGGT
TCGGGTTTTT

How do I use bash grep to get the second record ? In other languages one might use: 

>chr2\n([AGCTNagctn]*\n)*

In Bash I was trying to use the ideas from here (among other SOs). This did not work:

grep -zo '>chr2[AGCTNacgtn]+' file

Result should be:

>chr2
TTGNACACCC
TGGGGGAGTA

SOLUTION

On my system this was the solution (Almost Cyrus' below, i.e. with out the pipe to a second grep . ):

grep -Pzo '>chr1\n[AGCTNacgtn\n]+' file

Upvotes: 2

Views: 8312

Answers (6)

Venkateswara Rao
Venkateswara Rao

Reputation: 5392

Created sedgrep mixed version to support in generic way... You could use this sedgrep shell command available at https://github.com/iamdvr/sedgrep-shell-util

Direct Link: https://github.com/iamdvr/sedgrep-shell-util/blob/main/sedgrep

For your case direct command is this...

cat <FILE_NAME> | sed -nr ':main; /^>.*chr2/ { :loop; p; n; /^>/ b main; b loop} '

sedgrep usage is as follows...

Default NEW_LINE_PATTERN is ^\[
Usage : 
    cat {INPUT_FILE_NAME}  | sedgrep  {NEW_LINE_PATTERN} {THREAD_OR_SEARCH_PATTERN} 
    cat {INPUT_FILE_NAME}  | sedgrep  {THREAD_OR_SEARCH_PATTERN} 
    sedgrep {NEW_LINE_PATTERN} {THREAD_OR_SEARCH_PATTERN} {INPUT_FILE_NAME}
    sedgrep {THREAD_OR_SEARCH_PATTERN} {INPUT_FILE_NAME}
Example : 
    cat sampleInput.log | sedgrep 2016-05-23 DB_CONN
    cat sampleInput.log | sedgrep DB_CONN
    sedgrep 2016-05-23 DB_CONN sampleInput.log
    sedgrep DB_CONN sampleInput.log

Upvotes: 0

Dudi Boy
Dudi Boy

Reputation: 4865

The best tool for working with multi-line records is awk.

In your case:

awk 'BEGIN{RS=">"} NR==2 {print RS$0}' input.txt

input.txt

>chr1
AGCTACTTTT
AGGGNGGTNN
>chr2
TTGNACACCC
TGGGGGAGTA
>chr3
TGACGTGGGT
TCGGGTTTTT

Explanation:

BEGIN{RS=">"} Initially set record separator to ">"

NR==2 filter for record #2 only

{print RS$0} print record #2 with the missing record separator back

Upvotes: 0

VIPIN KUMAR
VIPIN KUMAR

Reputation: 3137

Try this - 

grep 'chr2' -A 2 file
>chr2
TTGNACACCC
TGGGGGAGTA

Upvotes: 0

clt60
clt60

Reputation: 63902

You should install the FAST perl package. It contains many utilities directly usable from the shell for dealing with fasta files, like fashead or fastail (and much more)

after installing it is simple as:

fashead -n2 fastafile | fastail -n1

output

>chr2
TTGNA.....

or even simpler

fasgrep chr2 fastafile

with the same output...

Upvotes: 1

Cyrus
Cyrus

Reputation: 88601

With GNU grep:

grep -Pzo '>chr2\n[AGCTNacgtn\n]+' file | grep .

Output:

>chr2
TTGNACACCC
TGGGGGAGTA

Upvotes: 3

anubhava
anubhava

Reputation: 785146

You can use awk with custom RS:

awk -v n=2 -v RS='(^|\n)>' 'NR==n+1{print ">" $0}' file    
>chr2
TTGNACACCC
TGGGGGAGTA

Upvotes: 2

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