grep (bash) multi-line pattern

Question

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]),

Answer 1

With GNU grep:

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

Output:

>chr2
TTGNACACCC
TGGGGGAGTA

Answer 2

Try this -

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

Answer 3

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...

Answer 4

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

Answer 5

You can use awk with custom RS:

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

Answer 6

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