Splitting a Multi-FASTA file into individual files
There are a number of things in here which make the code somewhat hard to read. Also, there's a big bug.

Bug

You never reset the $seq_obj variable. As a result, each time you add a new file you are actually adding the new data to the end of the old data too. Thus, your files get bigger, and bigger, etc.

Thus, the third sequence in your input:

&gt;gi|402898625|ref|XP_003912321.1| PREDICTED: cellular tumor antigen p53 [Papio anubis]
MEEPQSDPSIEPPLSQETFSDLWKLLPENNVLSPLPSQAVDDLMLSPDDLAQWLTEDPGPDEAPRMSEATPPMAPTPAAP
KPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSSHLKSKKGQSTSRHKKFMFKTEGPDSD


actually produces the output:

&gt;gi|402898625|ref|XP_003912321.1| PREDICTED: cellular tumor antigen p53 [Papio anubis]
MEEPQSDPSIEPPLSQETFSDLWKLLPENNVLSPLPSQAVDDLMLSPDDLAQWLTEDPGP
DEAPRMSEAAPHMAPTPAAPKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPA
GSRAHSSHLKSKKGQSTSRHKKFMFKTEGPDSDMEEPQSDPSIEPPLSQETFSDLWKLLP
ENNVLSPLPSQAVDDLMLSPDDLAQWLTEDPGPDEAPRMSEAAPPMAPTPAAPSCMGGMN
RRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENFRKKGEPCHELPPGSTKRA
LPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPAGSRAHSS
HLKSKKGQSTSRHKKFMFKTEGPDSDMEEPQSDPSIEPPLSQETFSDLWKLLPENNVLSP
LPSQAVDDLMLSPDDLAQWLTEDPGPDEAPRMSEATPPMAPTPAAPKPLDGEYFTLQIRG
RERFEMFRELNEALELKDAQAGKEPAGSRAHSSHLKSKKGQSTSRHKKFMFKTEGPDSD


which is the accumulation of all the previous inputs too. I have spent 20 minutes trying to figure out why my code is wrong.... but it's your code.



Better system

Additionally, the process you have 'batches' the data in one variable, and then dumps the variable when all the data is read.

If you reverse the algorithm, and open a file when the header arrives, and then write all the data (that's not a header) to that file, then the process would be simpler.

Additionally, you should use the 'diamond' magic filehandle &lt;&gt; for ease of use:


  The null filehandle &lt;&gt; is special: it can be used to emulate the
  behavior of sed and awk, and any other Unix filter program that takes
  a list of filenames, doing the same to each line of input from all of
  them. Input from &lt;&gt; comes either from standard input, or from each
  file listed on the command line.


So, if I break your code in to three sections. One section closes an open file, the next section starts a new file, and then a simple loop that checks to see whether it should start a new file, the code is much simpler.

Note also the general lack of global variables. Also, the 'id' line is not printed to the file when the file is created, but rather after the file is created as part of the 'normal' loop.

Finally, the process below copies the input lines unchanged from the input to the output. Your code 'reformats' the lines to 56 chars wide. This code does not do the reformat. I consider this to be a feature because of two things:


preserving input format is generally a good idea.
it saves having to chomp every line
it allows the data to be processed 1 line at a time, instead of batching it


If that does not work for you, then the code will have to be changed significantly.

#!/usr/bin/perl

use strict;
use autodie;

sub flushfile {
    my $file = shift;
    return undef unless $file;
    close $file;
    return undef;
}

sub makefile {
    my $control = shift;
    chomp $control;


    my @parts = split( /\h+/, $control, 2);
    my $f_name = $parts[0];
    $f_name =~ s/\|/_/g;
    $f_name =~ s/^&gt;//;
    $f_name =~ s/\_$//;
    $f_name .= ".fasta";

    print "Processing $f_name from $control\n";

    open (my $ofile, '&gt;', $f_name);
    return $ofile;
}

my $outfile;
while (&lt;&gt;) {

    if (/^&gt;/) {
        $outfile = flushfile($outfile);
        $outfile = makefile($_);
    }

    $outfile or die "Unexpected input: $_";
    print {$outfile} $_;
}
flushfile($outfile);




Line Trimming version

I have written it again using a system that does the line sizing too.

The following code is different. It accumulates partial lines and the outputs them when they are full. It also needs to print the control line first because that cannot be line-trimmed.

#!/usr/bin/perl

use strict;
use autodie;

my $linesize = 60;

sub flushfile {
    my $file = shift;
    my $partial = shift;
    return undef unless $file;
    print {$file} $partial . "\n";
    close $file;
    return undef;
}

sub makefile {
    my $control = shift;
    chomp $control;

    my @parts = split( /\h+/, $control, 2);
    my $f_name = $parts[0];
    $f_name =~ s/\|/_/g;
    $f_name =~ s/^&gt;//;
    $f_name =~ s/\_$//;
    $f_name .= ".fasta";

    print "Processing $f_name from $control\n";
    open (my $ofile, '&gt;', $f_name);
    print {$ofile} $control . "\n";
    return $ofile;
}

sub addline {
    my $file = shift;
    my $part = shift;
    my $nxt = shift;
    $file or die "Unexpected input: $nxt";

    $part .= $nxt;
    while (length($part) &gt;= $linesize) {
        my $front = substr ($part, 0, $linesize);
        #print "Printing $front\n";
        print {$file} ($front , "\n");
        $part = substr ($part, $linesize);
    }
    return $part;
}

my ($partial, $outfile);
$partial = "";
while (&lt;&gt;) {

    chomp;

    if (/^&gt;/) {
        $outfile = flushfile($outfile, $partial);
        $outfile = makefile($_);
    } else {
        $partial = addline($outfile, $partial, $_);
    }
}
flushfile($outfile, $partial);