Okay. You want the snoRNA text used as the primary key. Output like this? 

C:\test>junk55
{
  "snoRNA 10" => [
        {
          Nm_id     => "NM_001040105",
          exon      => 3,
          gene_id   => 91982771,
          gene_name => "Homo sapiens mucin 17, cell surface associated
+ (MUC17), mRNA.",
          seqs      => [
                         { query => [4, "TGGAGTCAAT", 13], sbjct => [4
+854, "TGGAGTCAAT", 4845] },
                       ],
          web_link  => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=R
+etrieve&db=nucleotide&dopt=GenBank&RID=UDU305DZ01N&log%24=nuclalign&b
+last_rank=97&list_uids=91982771",
        },
      ],
  "snoRNA 25, 26 and 27" => [
        {
          Nm_id     => "NM_001100162",
          exon      => 3,
          gene_id   => 154448895,
          gene_name => "Homo sapiens exportin 7 (XPO7), transcript var
+iant 3, mRNA.",
          seqs      => [
                         {
                           query => [2, "CCTGGAGTCGAGTG", 15],
                           sbjct => [146, "CCTGGAGTCGAGTG", 133],
                         },
                       ],
          web_link  => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=R
+etrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&b
+last_rank=2&list_uids=154448895",
        },
        {
          Nm_id     => "NM_002458",
          exon      => 31,
          gene_id   => 153945877,
          gene_name => "Homo sapiens mucin 5B, oligomeric mucus/gel-fo
+rming (MUC5B), mRNA.",
          seqs      => [
                         {
                           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],
                         },
                       ],
          web_link  => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=R
+etrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&b
+last_rank=9&list_uids=153945877",
        },
        {
          Nm_id     => "NM_206862",
          exon      => 4,
          gene_id   => 150418008,
          gene_name => "Homo sapiens transforming, acidic coiled-coil 
+containing protein 2 (TACC2), transcript variant 1, mRNA.",
          seqs      => [
                         {
                           query => [1, "ACCTGGAGTCGAG", 13],
                           sbjct => [4775, "ACCTGGAGTCGAG", 4763],
                         },
                       ],
          web_link  => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=R
+etrieve&db=nucleotide&dopt=GenBank&RID=UDW41RSS01S&log%24=nuclalign&b
+last_rank=10&list_uids=150418008",
        },
      ],
}

[download]

If so, then the changes required from Re: split a file into records and process it are minimal: 

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

my %records;
until( eof( DATA ) ) {
    my %record;
    ## put the exon number inside the record
    ( $record{ exon } ) = ( <DATA> =~ m[(\d+)] ); 

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

    ( $record{ gene_id } ) = ( $line =~ m[GI:(\d+)] );

    ( $record{ Nm_id } ) = ( <DATA> =~ m[(NM_\d[\d]+)] );

    ## save the snoRNA text...
    chomp( my $snoRNA_key = <DATA> );

    for( 1 .. $seqs ) {
        my $query = [ split ' ', <DATA> ]; shift @$query;
        scalar (<DATA>);
        my $sbjct = [ split ' ', <DATA> ]; shift @$sbjct;
        push @{ $record{ seqs } }, { query => $query, sbjct => $sbjct 
+};
    }

    chomp( $record{ gene_name } = <DATA> );

    chomp( $record{ web_link  } = <DATA> );

    ## And use it as the primary key in the main hash
    push @{ $records{ $snoRNA_key } }, \%record;
}

pp \%records;

__DATA__

[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^5: 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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