Re^2: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file

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[@]}
[download]

ERROR:

zsh:1: command not found: sedinho

how to put a function in linux environment accurately ??

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Re^3: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file by poj (Abbot) on Sep 11, 2017 at 12:27 UTC
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	[reply] [d/l]
Re^4: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file by Anonymous Monk on Sep 12, 2017 at 12:08 UTC
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.. :)	[reply] [d/l] [select]