Shell Programming and Scripting

Thanks for all your replies!!

I ran the one line awk script and turn out to be symbol">" is missing in the output file. How can I can the ">" remained in the very beginning like ">ref|NP_253535.1|"?

I'll also be nice if you can explain to me what is "vRS".

Thanks!!

gawk can, but not awk/nawk (at least not on Solaris).

---------- Post updated at 07:48 AM ---------- Previous update was at 07:45 AM ----------

see my previous post.

Well, UNIX optarg can be confusing, especially when awk has multi-letter commands in non sh style mixed in. Probably equivalent to "-v RS=...". I am not an optarg fan, as it makes things confusing to save a key stroke or two: training and mistakes are more expensive. For instance, "-abcde" might mean "-a 'bcde'" or "-a -b 'cde'" OR . . . "-a -b -c -d -e" depending on which if any one letter option takes an argument.

https://www.unix.com/man-page/All/3/optarg/

Looks like xpg4 awk or nawk (new awk) or the wrong O/S man page:

Man Page for awk (OpenSolaris Section 1) - The UNIX and Linux Forums

Code:

	

awk(1)				 User Commands				awk(1)

NAME
       awk - pattern scanning and processing language

SYNOPSIS
       /usr/bin/awk [-f progfile] [-Fc] [' prog '] [parameters]
	    [filename]...

       /usr/xpg4/bin/awk [-FcERE] [-v assignment]... 'program' -f progfile...
	    [argument]...

That woks! By the way, I don't have nawk on my mac and also linux red hat, so I use awk instead.

A further question, I have a list of names in one file, how do I get each of those and put together into one file by your "nawk" command?

I tried it by a naive guess, but it didn't return anything in outfile. The "mylist" file is the name list of all the entry name.

Code:

for i in mylist ; do awk -v str='$i' '$0~str{print RS $0}' RS='>' fasta-outCT-beta-q1; done > outfile

Code:

while read i
do
  awk -v str="$i" '$0~str{print RS $0}' RS='>' fasta-outCT-beta-q1
done < mylist > outfile