Dear monks, My question is related to file parsing within while loops. I have a large file containing many individual files all in the same format.

I want to extract certain features from each file which mainly is easy. My problem is when I need to extract everything between two markers in the file. I am struggling to get all the nice info between ORIGIN and // in each file.

This is how the file looks: How can I extract all the info between ORIGIN and // for each record?? 

# extract of file:  
#===============

FEATURES             Location/Qualifiers    
                     /note="blah blah"   
COUNT                200
ORIGIN
        1 lots of nice info
       61 lots of nice info
      121 lots of nice info
   
//

[download]
This is my code so far: 
open (FILE, $ARGV[0]) or die "unable to open FILE\n";
                                                                      
+                                          
my ($note, $info, $features,$count);
my ($c,$d);
my @seq;
my $in_seq = 0;
my $seq = '';
                                                                      
+                                          
while (<FILE>)     {
        my $line = $_;
      
        if ($line =~ /(FEATURES)\s+(\w+)/)   {
                $features = $2;
        }
        if ($line =~ /(COUNT)\s+(\d+)/)   {
                $count = $2;
        }
    
        if ($line =~ /^ORIGIN/)   {
        #        print "$line\n";
                push @seq, "$line\n";
        }     
        until ($line =~ /\/\/) {}; 
}
                                                                      
+                                          
print "@seq\n";

[download]

Retitled by davido.

In reply to Genbank file parsing by Anonymous Monk

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