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Full Discussion: How to append two fasta files?
Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303036080 by MadeInGermany on Thursday 13th of June 2019 04:57:26 PM
Old 06-13-2019
Post #5 is interesting.
I found it can be enhanced, by a ^ anchor (match at the beginning only), and by inserting a ^ character that becomes an anchor for the following grep
Code:
tr $'\n>' $' \n' <file1|  grep -vf <(sed -n 's/^>/^/p' file2) | cat  <(tr $'\n>' $' \n' <file2) - |  tr  -s $' \n' $'\n>'

Post #7 did not work for me.? Did not further analyze it.
Here is an embedded multi-line awk code that works for me:
Code:
#!/bin/sh
awk '
{
  ishead=($1~/^>/)
}
FNR==NR {
  # file1: store everything in F[head]
  if (ishead) {
     head=$1
     sep=""
  } else {
     F[head]=(F[head] sep $1)
     sep=ORS
  }
  next
}
{
  # file2: print everything, delete corresponding F[head] from file1
  if (ishead) {
    delete F[$1]
  }
  print
}
END {
  # print the remaining F[head] from file1
  for (head in F) {
    print head
    print F[head]
  }
}
' file1 file2

I chose $1 not $0 because I found some trailing spaces in the given examples; spaces are stripped if $1 is used.
 

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LEARN ABOUT DEBIAN

gchem3d

GCHEM3D(1)						       gnome-chemistry-utils							GCHEM3D(1)

NAME

       gchem3d - a small chemical viewer application

SYNOPSIS

       gchem3d [OPTION(S)...] [FILE...]

DESCRIPTION

       gchem3d is a small chemical viewer application, which can show several chemical file formats.

OPTIONS

       The following options are accepted:

       -b COLOR, --bgcolor=COLOR
	   Use the given color as background color.  COLOR can be one of "black" (default), "white", "#rrggbb" (don't forget to escape the "#"
	   character in the shell).

       -d MODEL, --display3d=MODEL
	   Choose how molecules are displayed.	MODEL can be one of "BallnStick" (default), "SpaceFill".

       -?, --help
	   Show application help options.

       --help-all, --help-*
	   Print all or just a group of help options. These options are not documented here. Instead see gtk-options(7) and gnome-options(7).

       -v, --version
	   Print gchem3d version information.

SEE ALSO

       gnome-options(7), gtk-options(7)

AUTHORS

       Jean Brefort <jean.brefort@normalesup.org>
	   Program author.

       Daniel Leidert <daniel.leidert@wgdd.de>
	   Manpage author.

COPYRIGHT

       Copyright (C) 2002-2007 Jean Brefort
       Copyright (C) 2004-2007 Daniel Leidert

       Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or any
       later version published by the Free Software Foundation.

gcu 0.12				      $Date: 2009-03-19 10:53:47 +0100 (jeu. 19 mars 2009) $					GCHEM3D(1)
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