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Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303035982 by vgersh99 on Tuesday 11th of June 2019 12:05:52 PM
Old 06-11-2019
not sure if I follow your samples and the desired output, but I think you might want this.

awk -f dinesh.awk file2 file1 where dinesh.awk is:
Code:
FNR==NR {
  if (FNR%2)
     head=$0
  else
     f2[head]=$0
  next
}
{
  if (FNR%2) {
     head=$0
     print
  }
  else
     print (head in f2)? f2[head] : $0
}

results in:
Code:
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG


Last edited by vgersh99; 06-11-2019 at 01:37 PM..
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HEAD(1) 								FSF								   HEAD(1)

NAME
head - output the first part of files SYNOPSIS
head [OPTION]... [FILE]... DESCRIPTION
Print first 10 lines of each FILE to standard output. With more than one FILE, precede each with a header giving the file name. With no FILE, or when FILE is -, read standard input. Mandatory arguments to long options are mandatory for short options too. -c, --bytes=SIZE print first SIZE bytes -n, --lines=NUMBER print first NUMBER lines instead of first 10 -q, --quiet, --silent never print headers giving file names -v, --verbose always print headers giving file names --help display this help and exit --version output version information and exit SIZE may have a multiplier suffix: b for 512, k for 1K, m for 1 Meg. AUTHOR
Written by David MacKenzie. REPORTING BUGS
Report bugs to <bug-coreutils@gnu.org>. COPYRIGHT
Copyright (C) 2002 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU- LAR PURPOSE. SEE ALSO
The full documentation for head is maintained as a Texinfo manual. If the info and head programs are properly installed at your site, the command info head should give you access to the complete manual. head (coreutils) 4.5.3 February 2003 HEAD(1)
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