How do you define a 'sequence'? How can you tell when you've moved from one to another? Are the sequences listed in series, or are they mixed together in some way? And while I'm at it, what have you tried and what didn't work? See How do I post a question effectively?.

In terms of transforming one file to a series of files, your code might look something like: 

my $fh;
my $i = 0;
while (my $line = <$in>) {
    if (new_sequence_test($line)) {
        $i++;
        open $fh, '>', "seq_$i" or die "Open fail seq_$i: $!\n"; 
    }
    print $fh $line;
}

[download]

Update: Now that you've added input and code, I can say a little more. First, while not strictly necessary, strict will help you catch a lot of potential issues and will make variable scoping intent more obvious. See Use strict warnings and diagnostics or die.

When you say while($seq=<IN>), you read in one line of your file. Your split assumes you are slurping your whole file. And especially if file is 'huge', you probably don't want to store it all in memory. Assuming your sequences are split by empty lines, you could modify my already posted code to accomplish your task. 

my $fh;
my $i = 0;
while (my $line = <$in>) {
    if (!$fh or $line !~ /\S/) {
        $i++;
        open $fh, '>', "seq_$i" or die "Open fail seq_$i: $!\n"; 
    }
    print $fh $line;
}

[download]

You could also do this very simply by modifying $/, but I suspect that solution would be unclear to you.

#11929 First ask yourself `How would I do this without a computer?' Then have the computer do it the same way.

In reply to Re: put every sequence of a file in a different output file by kennethk
in thread put every sequence of a file in a different output file by bingalee

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