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Top Forums Shell Programming and Scripting Fgrep or grep or awk help - scanning for delimiters. Post 302401480 by radoulov on Saturday 6th of March 2010 09:36:50 AM
Old 03-06-2010
Note that some awk implementations have problems with long multiline records (high number of bytes in the < blocks, in this case).

With Perl, I'm not able to come up with more concise solution than this one:

Code:
perl -ne'
  @_{/([^\n]+)/} = 1 and next if @ARGV;
  if (/^>/ or eof) {
    @_{$x =~ /^>([^ \/]+)/} and print $x;
    $x = "";
    } 
  $x .= $_' hitfile.txt FASTA.txt

You can modify the input record separator $/ with Perl too, but, as far as I know, not the way awk allows you to.

Last edited by radoulov; 03-06-2010 at 11:39 AM..
 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
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