Hi guys,
I am just learning perl (my 1st computer language) and am having some trouble with a simple script.
I am trying to split a large genbank file into individual sequence files. The individual sequence files need to look like this...
>"accession #"_"biotype"<br>
^^<br>
"sequence"<br>
<br>

[download]
and the name of these files should be
"accession#_biotype.seq"

Here is my script...
use strict;
use warnings;

# Constants
my $genfile = "c:\bemisia_coi.gb";
my $outfile = "$accession_$biotype";
my ($OUT, $IN);
my $line;

print "Input: $genfile\n";
open($IN, "$genfile") or die "cannot open $genfile\n";

while ($line = <$IN>) {
   $line = lc $line; #case insensitive
   my @line = split(/\///,$line);
      foreach my $i (0..$#line) {
         my $accession = "/locus\s*([a-z]{8})";
         my $biotype = "/biotype: ([a-z]{1})";
         my $sequence = "/origin(\*+)\//\";
            $sequence =~ s/\s//g; #Removing spaces
            $sequence =~ s/\d//g; #Removing numbers

open($OUT, '>' "$outfile") or die "cannot open $outfile \n";

print "Printing to $outfile \n";

print($OUT ">$accession_$biotype/n^^/n$sequence");

   }
}

[download]
Im getting tons of error that I think have to deal with local/global variables but I can't figure out, so any help is greatly appreciated!!!

In reply to Spltting Genbank File by perl_n00b

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