How to get matching pattern along with ID in a single command in grep? I have a file containing multiple fast sequneces. For a specific consensus pattern as input, I extracted all the matching patterns from target fasta sequences with
grep -o -E &quot;CC[GT]AAA[GC][AC]TT[GC]&quot; input.fasta

However, the above command will retrieve just the matching sequences from fasta sequences and I  also wanted to get the corresponding fasta header of each match.
For example, if input.fasta  file is something like this,
&gt;Gene 1
TGATGAAAAATGATAGAT
ATTGGGGGAAAAAAAAAT

&gt;Gene 2
TTTCCTAAAGATTGT
AAATTTAAAAATGTTTTT

(Gene 2 has matching subsequence CCTAAAGATTG)
Output:
CCTAAAGATTG   Gene2

I prefer a solution with grep. But other possible solutions also helpful.
Use this Perl one-liner:
perl -lne '$id = $1 if /^&gt;(.+)/; ($m) = /(CC[GT]AAA[GC][AC]TT[GC])/; print join &quot;\t&quot;, $id, $m if $m;' input.fasta

The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-n : Loop over the input one line at a time, assigning it to $_ by default.
-l : Strip the input line separator (&quot;\n&quot; on *NIX by default) before executing the code in-line, and append it when printing.
SEE ALSO:
perldoc perlrun: how to execute the Perl interpreter: command line switches