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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 don't think so. I suppose you have a large file containing info related to many individual files.
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
   
//
If you can rely on this format, here's how I'd do it:
#!/usr/bin/perl -ln use strict; use warnings; if ($_ eq 'ORIGIN') { local $/='//'; print <>; }
or
#!/usr/bin/perl -ln use strict; use warnings; print if $_ eq 'ORIGIN' .. $_ eq '//' __END__
Of course these are intended to be as minimal examples: adapt the techniques shown here to your needs.
This is my code so far:
open (FILE, $ARGV[0]) or die "unable to open FILE\n";
Why not using <> in the first place? Also, you'd better:
  • use lexical FHs,
  • use the three args form of open(),
  • put relevant info in the error message (i.e. at least include $!).
Note: I skipped the rest

In reply to Re: Genbank file parsing by blazar
in thread Genbank file parsing by Anonymous Monk

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