Re^3: skipping lines when parsing a file

Perhaps I do not understand your requirements. It would help if you were to also post your desired output. Here is an example using range operators:

use strict;
use warnings;

while (<DATA>) {
    print unless (/COMMENT/ .. /FEATURES/);
    print if (/FEATURES/);
}

__DATA__
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.
COMMENT     This sequence was annotated by the Ensembl system. Please 
+visit
            the Ensembl web site, http://www.ensembl.org/ for more
            information.
            All feature locations are relative to the first (5') base 
+of the
            sequence in this file. The sequence presented is always th
+e
            forward strand of the assembly. Features that lie outside 
+of the
            sequence contained in this file have clonal location coord
+inates
            in the format: <clone accession>.<version>:<start>..<end>
            The /gene indicates a unique id for a gene,
            /note="transcript_id=..." a unique id for a transcript,
            /protein_id a unique id for a peptide and note="exon_id=..
+." a
            unique id for an exon. These ids are maintained wherever p
+ossible
            between versions.
            All the exons and transcripts in Ensembl are confirmed by
            similarity to either protein or cDNA sequences.
            Features not parsed:
                 gene            AL807811.9.1.249021:69347..168228
            /locus_tag="Capzb" /gene="ENSMUSG00000028745" /note="cappi
+ng protein
            (actin filament) muscle Z-line, beta [Source:MGI;Acc:MGI:1
+04652]"
                 mRNA            join(complement(42593..42690),
            AL807811.9.1.249021:115325..115414,
            AL807811.9.1.249021:133677..133798,
            AL807811.9.1.249021:138400..138513,
            AL807811.9.1.249021:156412..156553,
            AL807811.9.1.249021:156884..157000,
            AL807811.9.1.249021:163445..163510,
            AL807811.9.1.249021:164172..164248,
            AL807811.9.1.249021:167419..168228) /gene="ENSMUSG00000028
+745"
            /note="transcript_id=ENSMUST00000102508"
                 CDS             join(complement(42593..42595),
            AL807811.9.1.249021:115325..115414,
            AL807811.9.1.249021:133677..133798,
            AL807811.9.1.249021:138400..138513,
            AL807811.9.1.249021:156412..156553,
            AL807811.9.1.249021:156884..157000,
            AL807811.9.1.249021:163445..163510,
            AL807811.9.1.249021:164172..164248,
            AL807811.9.1.249021:167419..167506) /db_xref="CCDS:CCDS188
+41.1"
            /db_xref="MGI:Capzb"
            /db_xref="Vega_mouse_transcript:OTTMUST00000022955"
            /protein_id="ENSMUSP00000099566" /gene="ENSMUSG00000028745
+"
            /note="transcript_id=ENSMUST00000102508"
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]

This is the output:

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]

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