my %data;
while (my $rec = fetch_record($fh)) {
    my $id = $rec->{id};
    push @{$data{$id}}, $rec->{sequence};
}
for my $id (keys %data) {
    print "$id ";
    print "$_\n" for @{$data{$id}};
}
[download]

One last alternative would be to re-write the file merging all the rows for a record on one line. Next, sort the file so duplicate IDs are adjacent and then it should be straight forward to merge them. Since it appears each row is fixed length, recreating the original structure from a single line should be straight forward.

I'd use a similar approach to Limbic~Region, but I'd accumulate the blocks as strings rather than arrays as they consume considerably less space, which will put off the time when you need to use a multi-pass solution. Building an array of newly read IDs as you go, allows for retaining the original ordering on output.

This:

#! perl -slw
use strict;

my( $id, %accu, @order );

while( <DATA> ) {
    chomp;
    if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) {
        $id = $1;
        unless( exists $accu{ $id } ) {
            push @order, $id;
            $accu{ $id } = $2;
        }
        else {
            $accu{ $id } .= ' ' . $2;
        }
    }
    else {
        $accu{ $id } .= ' ' . $_;
    }
}

for my $key ( @order ) {
    printf "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $key 
+};
    print '';
}

__DATA__
5390_7_9   MEWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
EITRDFEKEN PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
5390_8_1   MKWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
EITRDFEKEN PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
5390_8_2   MEWYKKIGLL ATTALALFGL GACSNYGKSA DDTVTIEYFN QKKEMTKILE
EITRDFEKEN SKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
5390_7_9   MEWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
EITRDFEKEN PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
LSNKDYLKRV KNGYAEKYAV NEKVYNVPFT ANAYGIYYNK DKFEELGLKV PETWDEFEQL
5390_8_1   MKWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
5390_8_2   MEWYKKIGLL ATTALALFGL GACSNYGKSA DDTVTIEYFN QKKEMTKILE
EITRDFEKEN SKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
LSNKDYLKRV KNGYAEKYAV NEKVYNVPFT ANAYGIYYNK DKFEELGLKV PETWDEFEQL
[download]

Produces:

C:\test>junk35
5390_7_9   MEWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
EITRDFEKEN PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
MEWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE EITRDFEKEN
PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED LSNKDYLKRV
KNGYAEKYAV NEKVYNVPFT ANAYGIYYNK DKFEELGLKV PETWDEFEQL

5390_8_1   MKWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE
EITRDFEKEN PKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
MKWYKKIGLL ATTGLALVGL GACSNYGKSA DGTVTIEYFN QKKEMTKTLE

5390_8_2   MEWYKKIGLL ATTALALFGL GACSNYGKSA DDTVTIEYFN QKKEMTKILE
EITRDFEKEN SKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED
MEWYKKIGLL ATTALALFGL GACSNYGKSA DDTVTIEYFN QKKEMTKILE EITRDFEKEN
SKIKVKVVNV PNAGEVLKTR VLAGDVPDVV NIYPQSIELQ EWAKAGVFED LSNKDYLKRV
KNGYAEKYAV NEKVYNVPFT ANAYGIYYNK DKFEELGLKV PETWDEFEQL
[download]

Thanks Limbic~Region and BrowserUk for your good advice. I have had a quick go with BrowserUk's script and it seems to work OK. However, the merge is not so clean and results after the merge seem not to be in equal chunks (I have posted this on to my scratchpad). I am speculating that this will continue as > continue to add more block (i.e thousands). I have adapted your script as follows:

#! perl -slw
use strict;



if (scalar(@ARGV) != 1) {
    print "\n";
    print "Usage: script.pl <alignment file>";
    print "\n";
    exit();
  }

my ($FILENAME) = @ARGV; #read in file
open(DATA, $FILENAME);

my( $id, %accu, @order );

## remove existing files    
my $remove = "new_alignment_".$FILENAME;  #remove any existing results
+ file
    if (unlink($remove) == 1) {
                        print "Existing \"$remove\" file was removed\n
+";
                          }



## generate a temporary storage file    
my $outputfile = "new_alignment_".$FILENAME; #make a big file in which
+ the final results will be printed
    unless ( open(POS, ">>$outputfile") ) {
    print "Cannot open file \"$outputfile\" to write to!!\n\n";
        exit;
        }

while( <DATA> ) {
    chomp;
    if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) {
        $id = $1;
        unless( exists $accu{ $id } ) {
            push @order, $id;
            $accu{ $id } = $2;
        }
        else {
            $accu{ $id } .= ' ' . $2;
        }
    }
    else {
        $accu{ $id } .= ' ' . $_;
    }
}

for my $key ( @order ) {
    printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $
+key };
    print POS '';
}
[download]

I must also confess I do not understand the last bit of code:

for my $key ( @order ) {
    printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $
+key };
    print POS '';
}
[download]

Could you kindly please explain it to me.

PS: Still thinking of how to implement what Limbic~Region has pointed out.

$new_guy

Or you could try this version first:

#! perl -slw
use strict;

my( $id, %accu, @order );

while( <DATA> ) {
    chomp;
    if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) {
        $id = $1;
        unless( exists $accu{ $id } ) {
            push @order, $id;
            $accu{ $id } = $2;
        }
        else {
            $accu{ $id } .= ' ' . $2;
        }
    }
    else {
        my $pad = 10 - length() % 11;
        $accu{ $id } .= ' ' . $_ . ' ' x $pad;
    }
}

for my $key ( @order ) {
    printf "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $key 
+};
    print '';
}
[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.

However, the merge is not so clean and results after the merge seem not to be in equal chunks (I have posted this on to my scratchpad).

I missed this bit of your spec: "(except for the very last chunk at the end of each block which might be shorter than 10 letters)".

Looks like you'll have to use Limbic~Region's solution of splitting the lines and storing the data as arrays.

---

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.