Re^3: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file

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];
}
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poj

Comment on Re^3: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file Download Code

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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]

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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]

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

$ mkdir test

execute:

Cheers.. :)

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