Hi there

I am trying to write a script to replace ID names from a FILE2.txt (that contains a series of DNA sequences formatted as below) with ID names from a FILE1.txt (that contains a single column filled with rows of names).

Here's what FILE2.txt looks like: 

 
>BAR12149;size=134;
ATTGGCCAAATTG.....
>BAR1524;size=1535;
TTAAGGCCTTAAT.....
...etc/

[download]

Here's what FILE2.txt looks like: 

GOM_202
GOM_23
.....etc/

[download]

The ideal final output would be in this format: 

 
>GOM_202
ATTGGCCAAATTG.....
>GOM_23
TTAAGGCCTTAAT.....
.....ect/

[download]

I've written a script but I am a beginner with perl. Would anyone be able to help me with this? I would really appreciate any constructive comments! 

#!/usr/bin/perl 
use strict;
use warnings;

my @arr;

while (<>) {
    chomp;
    push @arr, $_ if length;
    last if eof;
}

while (<>) {
    print /^>/ ? shift(@arr) . "\n" : $_;
}

[download]

Thanks in advance!!

In reply to Replace ID names from FILE1 to FILE2 by jemo

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