I'm running Strawberry perl 5.20.2 on windowsx64. First day, just trying to take over some bioinformatics from a person leaving (I have no perl experience). Could you tell me what switches/options there are for the below script? I can get it to work (using >perl split_FASTA-no_overlap.pl "filename". But the output is just to the "terminal"? and I would like it to write the files to the directory for import into a sequencing program. Sorry if question is not in the correct form. Thanks.

 #! /opt/local/compbio/bin/perl5.8.0 -w

$size = 5000;
$overlap = 1;
$overlap_size = 0.00*$size;
$f = $ARGV[0];
local $/ = "\n>";
open(IN, "$f") || die "$f no\n";
while(<IN>){
    s/>//g;
    $id = ''; $annt = '';
    @ln = split /\n/;
    $defLine = shift @ln;
    $id = $1 if $defLine =~ /^(\S+)\s?/;
    $annt = $1 if $defLine =~ /^\S+\s+(.+)$/;
    $seq = join("",@ln);
    for(my $i=0; ($i*$size)<(length$seq); $i++){
        $subSeq = substr($seq,$i*$size, $size);
        $subSeq =~ s/(\w{60)/\$1\n/g;
        chomp $subSeq;
        $start = $i*$size +1;
        $end = $start + (length$subSeq) - 1;
        print ">$id:[",$start,'-',$end,"] $annt\n$subSeq\n";
        if($overlap == 1 && ($i*$size+$overlap_size) < (length$seq)){
            $subSeq = substr($seq,$i*$size+$overlap_size, $size);
            $subSeq =~ s/(\w{60)/\$1\n/g;
            chomp $subSeq;
            $start = $i*$size +1+$overlap_size;
            $end = $start + (length$subSeq) - 1;
            print ">$id:[",$start,'-',$end,"] $annt\n$subSeq\n";
            
        }
    }
}

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In reply to begginer help running perl script by tstrobaugh

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