So it appears that sections of the file are defined by words in all caps starting in column 0. This actually lends itself pretty well to keeping track of the state (in this case the file section) you're in.

There are many other ways to do it, but this is an example of what I was suggesting:

my $state;

while (my $line=<$in>) {
    if ($line=~/^([A-Z]+)/) {
        $state=$1;
    }
    print $line unless $state eq "COMMENT";
}

[download]
which outputs: 
07:37<sandvik@sat1> ~/perl$ ./pmtest.pl
LOCUS       4                     302276 bp    DNA     linear   HTG 31
+-OCT-2008
DEFINITION  Mus musculus chromosome 4 NCBIM37 partial sequence
            138489260..138791535 reannotated via EnsEMBL
ACCESSION   chromosome:NCBIM37:4:138489260:138791535:-1
KEYWORDS    .
SOURCE      house mouse.
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Eutele
+ostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
            Sciurognathi; Muroidea; Muridae; Murinae; Mus.
FEATURES             Location/Qualifiers
     source          1..302276
                     /db_xref="taxon:10090"
                     /organism="Mus musculus"
     gene            complement(267261..268504)
                     /note="locus_tag=Rnf186"
                     /gene="ENSMUSG00000070661"
                     /note="ring finger protein 186 [Source:MGI;Acc:MG
+I:1914075]

[download]

In reply to Re^3: skipping lines when parsing a file by ssandv
in thread skipping lines when parsing a file by lomSpace

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