Dear monks,

I am trying to replace the headers of a multifasta file as input 1 by the set of new headers in input 2.

INPUT 1 could be for example:

>head1 \n seq1 \n >head2 \n seq2 \n

INPUT2 could be, for example

head1 \t headA \n headB \t headB \n

The FINAL output should be of the form

>headA \n seq1 \n >headB \n seq2 \n

This is the code I've have so far, but I have trouble when trying to use key value in hashes to extract out new header! Strange, what am I doing wrong?

note: I am a a very new to Perl programming

Thanks in advance to anyone who can help

use strict;
use warnings;

my @filenames = @ARGV;
my @output;
my (@headers_seqs, %head_seqs, %header_pairs, $destination);

open(IN1, '<', $filenames[0]) or die "Can't read from multifasta file 
+with alternating lines of headers and sequences $_: $! \n";
open(IN2, '<', $filenames[1]) or die "Can't read from tab-delimited he
+ader replacement file $_: $! \n";

while(<IN1>){
chomp;
if ($_=~ m/\>/)                                #looks for match to the
+ '>' character
    {
    my $header = $_;
#    print $header, "\n";
    $header =~ s/\>//;
    push @headers_seqs, $header;    
#    print "header:", "\t", $header, "\n";
    }
elsif ($_!~ m/\>/)                                #looks for match to 
+the '>' character
    {
    my $seq = $_;
#    print "seq:", "\t", $seq, "\n";
    push @headers_seqs, $seq;    
    }
}

print $#headers_seqs, "\n";
%head_seqs = @headers_seqs;


###########################***********************--------------------
+--------------------***********************##########################
+#

my @head_orig_new;

while(<IN2>){
chomp;

my @line_splits = split('\s+',$_);

#print "@line_splits", "\n";
my $orig_header = $line_splits[0];
#print $orig_header, "\n";
my $new_header = $line_splits[1]; 
#print $new_header, "\n";

push @head_orig_new, $orig_header;
push @head_orig_new, $new_header;

}


#print $#head_orig_new, "\n";
%header_pairs = @head_orig_new;

###########################***********************--------------------
+--------------------***********************##########################
+#

foreach(keys %head_seqs)
{
push @output, '>', $header_pairs{$_}, "\n";
push @output, $head_seqs{$_},"\n";
}

###########################***********************--------------------
+--------------------***********************##########################
+#    
    
$destination = $filenames[0].'_headers-replaced.fasta';

open (OUT, '>', $destination) or die "Can't write to file $destination
+: $!\n";    
print OUT @output;
close IN1;
close IN2;
close OUT;

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In reply to replace FASTA sequence headers by onlyIDleft

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