Hello onlyIDleft,

There are a number of problems with your code. For example, lines such as

%head_seqs = @headers_seqs;
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make no sense. You need to read up on perl data structures to understand arrays and hashes.

I think the following script does what you need:

use strict;
use warnings;

open(my $in1, '<', $ARGV[0])
    or die "Can't read from multifasta file '$ARGV[0]': $!";
my @multifasta = <$in1>;
close $in1;

open(my $in2, '<', $ARGV[1])
    or die "Can't read from header replacement file '$ARGV[1]': $!";
my %headers;

while (<$in2>)
{
    my ($orig, $new) = split;
    warn "Duplicate replacement: $orig --> $new\n" if exists $headers{
+$orig};
    $headers{$orig}  = $new;
}

close $in2;

my $destination = $ARGV[0] . '_headers-replaced.fasta';
open (my $out, '>', $destination)
    or die "Can't write to file '$destination': $!"; 

foreach my $line (@multifasta)
{
    if ($line =~ /^\>/)  # it is a header
    {
        foreach my $key (keys %headers)
        {
            if ($line =~ /$key/)
            {
                $line =~ s/$key/$headers{$key}/;
                last;
            }
        }
    }

    print $out $line;
}

close $out;
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HTH,

lines such as
%head_seqs = @headers_seqs;
make no sense.


It makes perfect sense.    Copying values between lists, arrays and hashes is a normal idiom in Perl.

            if ($line =~ /$key/)
            {
                $line =~ s/$key/$headers{$key}/;
                last;
            }
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Your $key values may contain regular expression meta-characters so you should use quotemeta on them.

Your loop exits on the first match but not necessarily the correct match.    You should anchor the patterns.

Thanks for your replies jwkrahn.

Actually, EACH of my values in the hash of new / old headers have # character in them, some of them have other special characters such as _ etc

I was under the impression that because my keys are all letter/number strings, that there should not be any problem with having special characters in the values, BUT not in the keys themselves

Am I missing something here about needing "quotemeta" for the hash's values as well?

I hope I am explaining the header pairs properly

Here is an example below:

cluster14621 \t Helitron#element_1

Thanks a lot Athanasius

There are so many ideas that are new to me here, from just one script of yours! Thanks :)

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my %lookup;
open my $fh, "<", 'input2.txt' or die $!;

while (<$fh>) {
    chomp;
    my ($id, $replace) = split /\t/;
    $lookup{$id} = $replace;
}
close $fh or die $!;

my $in  = Bio::SeqIO->new( -file   => "input1.txt" ,
                           -format => 'fasta');
my $out = Bio::SeqIO->new( -file   => '>test.dat',
                           -format => 'fasta');

while ( my $seq = $in->next_seq() ) {
    if (defined(my $replace = $lookup{ $seq->id })) {
        $seq->display_id($replace);
    }
    $out->write_seq($seq);
}

__END__
*** input 1
>chr1
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT
TTTATCTTTAGGCGGTATGCACTTTTAACAAAAAANNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC
CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCNNNN
>chrM
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAANAATTTCCACC
>GJKKTUG01DYDGC
GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGCCAAC
ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCAGCAG
ACATGAGGAATACAAACTACAATCTTTTACTTGATGATGCAATGCCGGACAAACTCTAGA
>F0Z7V0F01EDB3V
AAGGCGAGNGGTATCACGCAGTAAGTTACGGTTTTCGGGTAACGCGTCNGNGGNACTAAC
CCACGGNGGGTAACCCGTCNCTACCGGTATAGGACTAAGGTTACCGGAACGTCGTGGGGT
ACCCCCCGGACGGGGACCGTCCCCTCATANAGTCAACNGTNTGAGATGGACTAACTCAAA
CCTAGTTTCAAGTACTATTTAACTTACTTACGTTACCCGTAATTTCGGCGTTTAGAGGCG


*** input 2
chr1    headA
chrM    headB
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>headA
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA
AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTAGGCGGTATGC
ACTTTTAACAAAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA
TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCNNNN
>headB
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
GCAGTATCTGTCTTTGATTCCTGCCTCATTCTATTATTTATCGCACCTACGTTCAATATT
ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAANAATTTCCACC
>GJKKTUG01DYDGC
GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGCCAAC
ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCAGCAG
ACATGAGGAATACAAACTACAATCTTTTACTTGATGATGCAATGCCGGACAAACTCTAGA
>F0Z7V0F01EDB3V
AAGGCGAGNGGTATCACGCAGTAAGTTACGGTTTTCGGGTAACGCGTCNGNGGNACTAAC
CCACGGNGGGTAACCCGTCNCTACCGGTATAGGACTAAGGTTACCGGAACGTCGTGGGGT
ACCCCCCGGACGGGGACCGTCCCCTCATANAGTCAACNGTNTGAGATGGACTAACTCAAA
CCTAGTTTCAAGTACTATTTAACTTACTTACGTTACCCGTAATTTCGGCGTTTAGAGGCG
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Chris

It sounds like you want something like this:

use strict;
use warnings;

@ARGV == 2 or die "usage: $0 <multifasta file> <header replacement fil
+e>\n";

my ( $fasta_file, $header_file ) = @ARGV;
my $destination = $fasta_file . '_headers-replaced.fasta';

open IN2, '<', $header_file or die "Can't read from tab-delimited head
+er replacement file $header_file: $!\n";

my %head_seqs;
while ( <IN2> ) {
    chomp;
    my ( $old, $new ) = split /\t/;
    $head_seqs{ $old } = $new;
    }
close IN2;

open IN1, '<', $fasta_file or die "Can't read from multifasta file wit
+h alternating lines of headers and sequences $fasta_file: $!\n";

open OUT, '>', $destination or die "Can't write to file $destination: 
+$!\n";    

while ( <IN1> ) {
    if ( /^>(.+)$/ && exists $head_seqs{ $1 } ) {
        $_ = ">$head_seqs{ $1 }\n";
        }
    print OUT $_;
    }
close IN1;
close OUT;
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