Hey Alfredo, let's break down what's going wrong with your Perl script and fix it step by step to meet your goal: keeping header lines intact while merging all sequence lines for each entry into a single line (removing their line breaks).

What's Wrong with the Original Script? #

1. Broken Core Logic #

Your biggest issue is that you print $header.$seq."\n" every single loop iteration, regardless of whether you're processing a header or sequence line:

• When you hit a new header, you immediately print the new header paired with the previous entry's sequence, causing duplicate/incorrect output.
• For sequence lines, you overwrite $seq with just the current line instead of appending to it, so you never merge multiple sequence lines into one.

2. Redundant Chomping #

You run chomp $currentline twice (once at the top of the loop, again in the else branch) — this is unnecessary, since the first chomp already removes the line break from $currentline.

Fixed Script with Explanations #

Here's a revised version of your code that works as intended, with comments explaining key changes:

#!/usr/bin/perl
use strict;
use warnings; # Adds helpful error checking for edge cases

my $db = shift;
my $outfile = "Silva_chomped_for_R_fin.fasta";
my $header;
my $seq = ''; # Initialize empty sequence string
my $kick = '>'; # No need to escape > in single quotes

# Use lexical filehandles (safer than global ones) with error checking
open(my $FASTAFILE, '<', $db) or die "Failed to open input file: $!";
open(my $OUTFILE, '>', $outfile) or die "Failed to open output file: $!";

while (<$FASTAFILE>) {
    my $currentline = $_;
    chomp $currentline; # Remove line break from all lines once

    if ($currentline =~ /^$kick/) {
        # If we already have a header/sequence from a previous entry, print it first
        if (defined $header) {
            print $OUTFILE "$header\n$seq\n";
        }
        # Update to new header and reset sequence for the next entry
        $header = $currentline;
        $seq = '';
    } else {
        # Append sequence line to the existing sequence string (no line breaks)
        $seq .= $currentline;
    }
}

# Print the last entry (since the loop ends before printing it)
if (defined $header) {
    print $OUTFILE "$header\n$seq\n";
}

close $OUTFILE;
close $FASTAFILE;
exit;

Key Improvements #

• Lexical Filehandles: Using my $FASTAFILE instead of global handles is more secure and avoids conflicts.
• Proper Entry Handling: We only print a complete entry (header + merged sequence) when we hit a new header, ensuring each entry is formatted correctly.
• Sequence Merging: Sequence lines are appended to $seq instead of overwriting it, so all lines for one entry become a single line.
• Final Entry Print: The loop doesn't print the last entry, so we add an extra print statement after the loop to catch it.
• Header Line Preservation: Header lines retain their line breaks (we add \n when printing), while sequence lines are merged into one line.

Why Chomp Seemed Ineffective #

Your chomp was actually working, but your broken output logic made it look like it wasn't. By printing every iteration, you were outputting single sequence lines with newlines added back immediately, resulting in output that looked identical (or worse) than the original file.

内容的提问来源于stack exchange，提问作者Alfredo Mari