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Top Forums UNIX for Dummies Questions & Answers Finding specific series of strings or characters Post 302562620 by Corona688 on Friday 7th of October 2011 12:28:12 PM
Old 10-07-2011
Since the >sequence5 is part of the file, why not use > as the record separator? awk will read each thing in one whack instead of having to spread your logic across many different lines.

Code:
$ cat sequence.awk

BEGIN { RS=">"; FS="\n"; OFS="\n"; ORS=">" }

/-/ { if(!P++) printf("%s", ORS); print }

$ awk -f sequence.awk < data
>Sequence1
AGACAGATGACAGTAGACAGAT-GACGATAGCAGT
>Sequence4
AGACAGATGA-AGTAGACAGATTGACGATAGCAGT

/-/ matches records containing -. ! /-/ would match records not containing -. ! /[-*]/ would match records not containing * or -. And so forth.

The if(!P++) printf("%s", ORS); is to print the very first >, which would otherwise be missing.

Last edited by Corona688; 10-07-2011 at 01:35 PM..
 

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SHCOMP(1)						       Korn shell utilities							 SHCOMP(1)

NAME
shcomp - compile a shell script SYNOPSIS
shcomp [ options ] [infile [outfile]] DESCRIPTION
Unless -D is specified, shcomp takes a shell script, infile, and creates a binary format file, outfile, that ksh can read and execute with the same effect as the original script. Since aliases are processed as the script is read, alias definitions whose value requires variable expansion will not work correctly. If -D is specified, all double quoted strings that are preceded by $ are output. These are the messages that need to be translated to locale specific versions for internationalization. If outfile is omitted, then the results will be written to standard output. If infile is also omitted, the shell script will be read from standard input. OPTIONS
[D dictionary] Generate a list of strings that need to be placed in a message catalog for internationalization. [n noexec] Displays warn- ing messages for obsolete or non-conforming constructs. [v verbose] Displays input from infile onto standard error as it reads it. EXIT STATUS
0 Successful completion. >0 An error occurred. SEE ALSO
ksh(1) IMPLEMENTATION
version shcomp (AT&T Research) 2003-03-02 author David Korn <dgk@research.att.com> copyright Copyright (c) 1982-2010 AT&T Intellectual Property license http://www.opensource.org/licenses/cpl1.0.txt 2003-03-02 SHCOMP(1)
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