ChangeHeader

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long 'HelpMessage';

my $usage=<<_EOH_;;
------------------------------------------------------------------------------------------
This script is used to change the header of your read nb matrix according to you command
Usage: 
ChangeHeader --raw all_species_raw_nb_matrix.xls --rename rename.txt > all_species_raw_nb_rename.matrix.xls

Example:
1. --rename: rename.txt
B36  Common_Cn_1
B37  Common_Cn_2
B38  Common_Cn_3
B39  Common_Cn_4
B40  Common_Cn_5

2. --raw: all_species_raw_nb_matrix.xls
     B36  B37  B38  B39  B40  B6   B7   B8   B9   B10  B31  B32  B33  B34  B35  B1
OG0038649 1974 3000 2376 2194 2773 2573 2427 2451 2573 2264 2374 2288 2152 2436 2120 2556

                                                                           Kang 2021-09-02
------------------------------------------------------------------------------------------
_EOH_
;

GetOptions(
     'raw:s', \my $raw,  # the file whose header to be changed
     'rename:s', \ my $rename,     # the file including the old name (first column) and new name (second column)
     'help', \ my $help
     );

if ($help || (! $raw) && (! $rename) ) {
     die $usage; # all of these options are mandatory requirements
}

my %hash=&build_hash_name($rename);
my $i;
open FIL, "$raw" or die "can not open $raw\n"; # the file whose header will be changed
while (<FIL>) {
     chomp;
     $i++;
     my @a=split /\t/;
     if ($i==1) {
          my $header;
          for (my $j = 0; $j < @a; $j++) {
               $a[$j]=~s/\s+//g;
               my $name=$hash{$a[$j]}?$hash{$a[$j]}:$a[$j];
               $header.=$name."\t";
          }
          $header=~s/\s+$//;
          print "$header\n";
     } else {
          print "$_\n";
     }
}

sub build_hash_name {
     my ($file)=@_;
     my %hash;
     open FIL1, "$file" or die "can not open $file\n";
     while (<FIL1>) {
          chomp;
          my @a=split /\t/;
          my ($oldname, $newname)=($a[0], $a[1]);
          $oldname=~s/\s+//g;
          $newname=~s/\s+//g;
          $hash{$oldname}=$newname;
     }
     return %hash;
}