I've added an example of the input and output to my original post, and my code is currently looking like this, but again I am still not sure I am using the hash correctly, and the hash key is really throwing me. I'm not getting any errors with this code, but my output file is empty

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

open( INFILE, "<", 'myosin.fasta') or die $!; #open original myosin.fa
+sta for reading
open( OUTFILE, ">", 'modifiedHeaders.fasta') or die $!; #open/create n
+ew fasta for writing

my %headerHash; #create hash for the header
my $seq;
my $header;

#loop through old file 
while (<INFILE>){
        chomp;
        my $line = $_;
# use if/then to seperate headers from seq, while regex to select only
+ species name in header
                if ($line =~ /^>/){
                 $header = $line;
                        if ($header =~ /(>gi.*)\[(.+)\](>g.*)\[(.+)\]/
+){
                                my $headerHash = $2;
                                $headerHash{$2} = $2;
}
                        }
                else {
                 $seq = $line;

        }
}
close INFILE;
for my $key(keys %headerHash){

print OUTFILE $headerHash{$key}, "\n", $seq, "\n";
}

[download]

In reply to Re^2: While loop with nested if statements by lairel
in thread While loop with nested if statements by lairel

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