Then I'd suggest that rather than have a single loop reading lines, and then having conditionals to decide what to do with each type of line, you use a loop that terminates on eof and reads the individual lines of each record in line. This makes for a more robust parser with less confusing conditional code and line to line state.

This doesn't do the final extraction of the required parts from individual liens of the records, which is easily added, but serves to demonstrate the technique: 

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %records;
until( eof( DATA ) ) {
    chomp( my $exon = <DATA> );
    push @{ $records{ $exon } }, {};

    my $seqs = 1;
    my $line = <DATA>;
    if( $line =~ m[(\d+) different hits] ) {
        $seqs = $1;
        chomp( $records{ $exon }[ -1 ]{ gene_id } = <DATA> );
    }
    else {
        chomp( $records{ $exon }[ -1 ]{ gene_id } = $line );
    }

    chomp( $records{ $exon }[ -1 ]{ Nm_id } = <DATA> );

    chomp( $records{ $exon }[ -1 ]{ snoRNA_key } = <DATA> );

    for( 1 .. $seqs ) {
        chomp( my $query = <DATA> );
        scalar (<DATA>);
        chomp( my $sbjct = <DATA> );
        push @{ $records{ $exon }[ -1 ]{ seqs } }, { $query => $sbjct 
+};
    }

    chomp( $records{ $exon }[ -1 ]{ gene_name } = <DATA> );

    chomp( $records{ $exon }[ -1 ]{ web_link  } = <DATA> );
}

pp \%records;

__DATA__
3
GI:91982771
NM_001040105.1
snoRNA 10
Query  4     TGGAGTCAAT  13
             ||||||||||
Sbjct  4854  TGGAGTCAAT  4845
Homo sapiens mucin 17, cell surface associated (MUC17), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&do
+pt=GenBank&RID=UDU305DZ01N&log%24=nuclalign&blast_rank=97&list_uids=9
+1982771
3
GI:154448895
NM_001100162.1
snoRNA 25, 26 and 27
Query  2    CCTGGAGTCGAGTG  15
            ||||||||||||||
Sbjct  146  CCTGGAGTCGAGTG  133
Homo sapiens exportin 7 (XPO7), transcript variant 3, mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&do
+pt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=2&list_uids=15
+4448895
31
4 different hits
GI:153945877
NM_002458.1
snoRNA 25, 26 and 27
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  6818  CTGGAGTCGAGTG  6806
Query  3     CTGGAGTCGAGTG  15
             |||||||||||||
Sbjct  8489  CTGGAGTCGAGTG  8477
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  10589  CTGGAGTCGAGTG  10577
Query  3      CTGGAGTCGAGTG  15
              |||||||||||||
Sbjct  12260  CTGGAGTCGAGTG  12248
Homo sapiens mucin 5B, oligomeric mucus/gel-forming (MUC5B), mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&do
+pt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=9&list_uids=15
+3945877
4
GI:150418008
NM_206862.2
snoRNA 25, 26 and 27
Query  1     ACCTGGAGTCGAG  13
             |||||||||||||
Sbjct  4775  ACCTGGAGTCGAG  4763
Homo sapiens transforming, acidic coiled-coil containing protein 2 (TA
+CC2), transcript variant 1, mRNA.
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&do
+pt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&blast_rank=10&list_uids=1
+50418008

[download]

Output: 

C:\test>junk55
{
  3  => [
          {
            Nm_id      => "NM_001040105.1",
            gene_id    => "GI:91982771",
            gene_name  => "Homo sapiens mucin 17, cell surface associa
+ted (MUC17), mRNA.",
            seqs       => [
                            {
                              "Query  4     TGGAGTCAAT  13" => "Sbjct 
+ 4854  TGGAGTCAAT  4845",
                            },
                          ],
            snoRNA_key => "snoRNA 10",
            web_link   => "http://www.ncbi.nlm.nih.gov/sites/entrez?cm
+d=Retrieve&db=nucleotide&dopt=GenBank&RID=UDU305DZ01N&log%24=nuclalig
+n&blast_rank=97&list_uids=91982771",
          },
          {
            Nm_id      => "NM_001100162.1",
            gene_id    => "GI:154448895",
            gene_name  => "Homo sapiens exportin 7 (XPO7), transcript 
+variant 3, mRNA.",
            seqs       => [
                            {
                              "Query  2    CCTGGAGTCGAGTG  15" => "Sbj
+ct  146  CCTGGAGTCGAGTG  133",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "http://www.ncbi.nlm.nih.gov/sites/entrez?cm
+d=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalig
+n&blast_rank=2&list_uids=154448895",
          },
        ],
  4  => [
          {
            Nm_id      => "NM_206862.2",
            gene_id    => "GI:150418008",
            gene_name  => "Homo sapiens transforming, acidic coiled-co
+il containing protein 2 (TACC2), transcript variant 1, mRNA.",
            seqs       => [
                            {
                              "Query  1     ACCTGGAGTCGAG  13" => "Sbj
+ct  4775  ACCTGGAGTCGAG  4763",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "http://www.ncbi.nlm.nih.gov/sites/entrez?cm
+d=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalig
+n&blast_rank=10&list_uids=150418008",
          },
        ],
  31 => [
          {
            Nm_id      => "NM_002458.1",
            gene_id    => "GI:153945877",
            gene_name  => "Homo sapiens mucin 5B, oligomeric mucus/gel
+-forming (MUC5B), mRNA.",
            seqs       => [
                            {
                              "Query  3     CTGGAGTCGAGTG  15" => "Sbj
+ct  6818  CTGGAGTCGAGTG  6806",
                            },
                            {
                              "Query  3     CTGGAGTCGAGTG  15" => "Sbj
+ct  8489  CTGGAGTCGAGTG  8477",
                            },
                            {
                              "Query  3      CTGGAGTCGAGTG  15" => "Sb
+jct  10589  CTGGAGTCGAGTG  10577",
                            },
                            {
                              "Query  3      CTGGAGTCGAGTG  15" => "Sb
+jct  12260  CTGGAGTCGAGTG  12248",
                            },
                          ],
            snoRNA_key => "snoRNA 25, 26 and 27",
            web_link   => "http://www.ncbi.nlm.nih.gov/sites/entrez?cm
+d=Retrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalig
+n&blast_rank=9&list_uids=153945877",
          },
        ],
}

[download]
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
"I'd rather go naked than blow up my ass"

In reply to Re^3: split a file into records and process it by BrowserUk
in thread split a file into records and process it by biohisham

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