A more complete parser now we've established the data format:

(Updated: simplified the references, by using a local %record during parsing. Same output)

(Update2: Removed need for duplicated Gene_id regex.)

(Update3: Corrected dumb context assignment error introduced during simplification.) 

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

my %records;
until( eof( DATA ) ) {
    my %record;
    chomp( my $exon = <DATA> );

    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]+)] );

    push @{ $record{ snoRNA_key } }, ( <DATA> =~  m[(\d+)]g );

    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> );

    push @{ $records{ $exon } }, \%record;
}

pp \%records;

__DATA__

[download]

Output:

C:\test>junk55
{
  3  => [
          {
            Nm_id      => "NM_001040105",
            gene_id    => 91982771,
            gene_name  => "Homo sapiens mucin 17, cell surface associa
+ted (MUC17), mRNA.",
            seqs       => [
                            { query => [4, "TGGAGTCAAT", 13], sbjct =>
+ [4854, "TGGAGTCAAT", 4845] },
                          ],
            snoRNA_key => [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",
            gene_id    => 154448895,
            gene_name  => "Homo sapiens exportin 7 (XPO7), transcript 
+variant 3, mRNA.",
            seqs       => [
                            {
                              query => [2, "CCTGGAGTCGAGTG", 15],
                              sbjct => [146, "CCTGGAGTCGAGTG", 133],
                            },
                          ],
            snoRNA_key => [25, 26, 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",
            gene_id    => 150418008,
            gene_name  => "Homo sapiens transforming, acidic coiled-co
+il containing protein 2 (TACC2), transcript variant 1, mRNA.",
            seqs       => [
                            {
                              query => [1, "ACCTGGAGTCGAG", 13],
                              sbjct => [4775, "ACCTGGAGTCGAG", 4763],
                            },
                          ],
            snoRNA_key => [25, 26, 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",
            gene_id    => 153945877,
            gene_name  => "Homo sapiens mucin 5B, oligomeric mucus/gel
+-forming (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]
+,
                            },
                          ],
            snoRNA_key => [25, 26, 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: split a file into records and process it by BrowserUk
in thread split a file into records and process it by biohisham

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.