well i have tried the following code:

i put the following function in linux enviroment: and(i guess problem is here but unbable to fix it )

function sedinho () { sed -i  "s/^.*\]/>$1/g" $2;}
export -f sedinho
[download]

create variables of : list of new headers (LIST1) list of input files (LIST2)

LIST1=($(cat Headers.txt))
LIST2=($(find /folder/with/fasta/files/ -maxdepth 0 -name "*CDS.fasta"
+ | sort))

parallel --xapply sedinho {1} {2} ::: ${LIST1[@]} ::: ${LIST2[@]}
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ERROR:

zsh:1: command not found: sedinho

zsh:1: command not found: sedinho

zsh:1: command not found: sedinho

how to put a function in linux environment accurately ??

This Perl script does the first part reading the filenames and headers into an array using File::Find. How is the order of the lines in Header.txt matched to these filenames/headers ?

#!/usr/bin/perl
use strict;
use File::Find;
use Data::Dumper;

my $folder = '/folder/with/fasta/files';

my @files=();
find( \&process, $folder );
print Dumper \@files;

sub process { 
  return unless $_ =~ /CDS\.fasta$/;
  my $file = $File::Find::name;
  open my $fh,'<',$file or die $!;
  my $header = <$fh>;
  close $fh;
  push @files,[$File::Find::dir,$_,$header];
}
[download]

poj

The mapping of names in Headers.txt and the FASTA files can work.

 Chimpanzee_AMY2B_CDS.fasta                 MP.C_AMY2B
Human_AMY2B_CDS.fasta                      FP.H_AMY2B
[download]

Following solution worked for my problem.

create a folder called test (in the same folder where fasta files are located) and run the command:

$ mkdir test

execute:

 for i in $(seq 1 $(ls *.fasta |wc -l)); do sed -n "$i"p headers.txt| sed 's/^/>/'> test/$(ls *.fasta| sed -n "$i"p); cat $(ls *.fasta| sed -n "$i"p)| sed '1d' >>test/$(ls *.fasta| sed -n "$i"p); done

Cheers.. :)