I'd do it this way: (This requires 5.8.x)

$str = 'MKTVEQTSPTMTSEKARWIY ... ELLTDVYVSYDHEGRNG';
print join ' ', unpack '(a10)*', $_ for unpack '(a50)*', $str;;

MKTVEQTSPT MTSEKARWIY QKMVEIRMFE DRVHDIFSKG EIPGFVHLYA
GEEAIAVGLC AHLDHNDYIT STHRGHGHCI AKGCELDGMM AEIYGKSTGL
CKGKGGSMHI ADLDRGMLGA NGIVGGGFTL AAGAALTAKF KQTGGVAVCF
FGDGANNQGT FHEGINLAAI WDLPVVFVAE NNGYGEATPF HYASACEQIT
DRAKGYNIPG VKVDGKDVVA VYEVAREAVE RARRGEGPTL IECITYRNYG
HFEGDAQTYK TGREKEEHTE ERDAITLFEK YALSNNLLTE EAIQTVRHEV
EQSVDRAVDF ANASDYPQPE ELLTDVYVSY DHEGRNG
[download]

Very nice (++) but aren't you missing the new line? ...

print join ' ', unpack '(a10)*', "$_\n" for unpack '(a50)*', $str;
[download]

update that newline is in the wrong place...

print "" . join ' ', unpack '(a10)*', $_ . "\n" for unpack '(a50)*', $
+str;
[download]

update A regex solution based on your plan of attack (if only because (un)?pack still scares me :)

for ($str =~ /.{1,50}/g) {print join " ", /.{1,10}/g; print "\n"}
[download]

---
my name's not Keith, and I'm not reasonable.

I habitually run perl with -l enabled (see perlrun), which has the effect of setting $/ =  "\n" (and $\ = "\n"), so print adds a newline automatically. Hence the output I posted is unmodifed.

This makes print (roughly?) equivalent to say in Perl 6.

I also seem to recall seeing a news item that suggested that this keyword would also be available in Perl 5 as of v5.10?

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

What have you tried? What problems are you having?

We're far more likely to help people who have tried to solve their problems for themselves first.

Have you looked at split? Or substr? Personally I think I'd use a regular expression.

Hi sanku, First thing is look into How (Not) To Ask A Question and How do I post a question effectively?, then you try like this,

use strict;
use warnings;

my $str = 'MKTVEQTSPTMTSEKARWIYQKMVEIRMFEDRVHDIFSKGEIPGFVHLYAGEEAIAVGL
+CAHLDHNDYITSTHRGHGHCIAKGCELDGMMAEIYGKSTGLCKGKGGSMHIADLDRGMLGANGIVGGGF
+TLAAGAALTAKFKQTGGVAVCFFGDGANNQGTFHEGINLAAIWDLPVVFVAENNGYGEATPFHYASACE
+QITDRAKGYNIPGVKVDGKDVVAVYEVAREAVERARRGEGPTLIECITYRNYGHFEGDAQTYKTGREKE
+EHTEERDAITLFEKYALSNNLLTEEAIQTVRHEVEQSVDRAVDFANASDYPQPEELLTDVYVSYDHEGR
+NG';

$str =~ s/(.{10})/$1 /gsi;
$str =~ s/((?:[^ ]+ ){5})/$1\n/gsi;

print $str;
[download]

davorg++

Updated : Thanks BrowserUK

Using $& (and friends) can be nasty. See Devel::SawAmpersand for why.

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

use strict;
use warnings;

my $string = q{MKTVEQTSPTMTSEKARWIYQKMVEIRMFEDRVHDIFSKGEIPGFVHLYAGEEAI
+AVGLCAHLDHNDYITSTHRGHGHCIAKGCELDGMMAEIYGKSTGLCKGKGGSMHIADLDRGMLGANGIV
+GGGFTLAAGAALTAKFKQTGGVAVCFFGDGANNQGTFHEGINLAAIWDLPVVFVAENNGYGEATPFHYA
+SACEQITDRAKGYNIPGVKVDGKDVVAVYEVAREAVERARRGEGPTLIECITYRNYGHFEGDAQTYKTG
+REKEEHTEERDAITLFEKYALSNNLLTEEAIQTVRHEVEQSVDRAVDFANASDYPQPEELLTDVYVSYD
+HEGRNG};

my $newString = q{};
my $count     = 0;

while (length $string >= 10)
{
    $count += 10;
    $newString .= substr $string, 0, 10, q{};
    $newString .=
       $count % 50
       ? q{ }
       : qq{\n};
}

$newString .= qq{$string\n};
print $newString;
[download]

and the output

MKTVEQTSPT MTSEKARWIY QKMVEIRMFE DRVHDIFSKG EIPGFVHLYA
GEEAIAVGLC AHLDHNDYIT STHRGHGHCI AKGCELDGMM AEIYGKSTGL
CKGKGGSMHI ADLDRGMLGA NGIVGGGFTL AAGAALTAKF KQTGGVAVCF
FGDGANNQGT FHEGINLAAI WDLPVVFVAE NNGYGEATPF HYASACEQIT
DRAKGYNIPG VKVDGKDVVA VYEVAREAVE RARRGEGPTL IECITYRNYG
HFEGDAQTYK TGREKEEHTE ERDAITLFEK YALSNNLLTE EAIQTVRHEV
EQSVDRAVDF ANASDYPQPE ELLTDVYVSY DHEGRNG
[download]

I hope this is of interest.

Cheers,

JohnGG

Update: Amended code to remove length test in last .= assignment as it would fail to append a newline if the string length was a multiple of 10 but not of 50. Original line

$newString .= qq{$string\n} if length $string;
[download]

If your question is how to convert a sequence file in fasta format to a sequence file in genbank format, then I'd suggest looking at Bio::SeqIO from BioPerl. That module makes formatting changes trivial:

use Bio::SeqIO;

my $in_obj  = Bio::SeqIO->newFh( '-file'   => $infile_name,
                                 '-format' => $infile_format );
my $out_obj = Bio::SeqIO->newFh( '-file'   => '>' . $outfile_name,
                                 '-format' => $outfile_format );

while( <$in_obj> )
{
    print $out_obj $_;
}
[download]

If you want a custom format based on the genbank format, you could tweak the Bio::SeqIO::GenBank module. The relevant section of code (based on your original description) is in the write_seq function:

    # print out the sequence
    my $nuc = 60;        # Number of nucleotides per line
    my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line
    my $out_pat   = 'A11' x 6; # Pattern for packing a line
[download]

$a=<>;
while ($a=~s/(\s?)(\w{10})(\w)/$1$2 $3/){}
$a=~s/((\w+\s){5})/$1\n/g;
print $a,"\n";
[download]

$ perl -le'
my $string = "MKTVEQTSPTMTSEKARWIYQKMVEIRMFEDRVHDIFSKGEIPGFVHLYAGEEAIA
+VGLCAHLDHNDYITSTHRGHGHCIAKGCELDGMMAEIYGKSTGLCKGKGGSMHIADLDRGMLGANGIVG
+GGFTLAAGAALTAKFKQTGGVAVCFFGDGANNQGTFHEGINLAAIWDLPVVFVAENNGYGEATPFHYAS
+ACEQITDRAKGYNIPGVKVDGKDVVAVYEVAREAVERARRGEGPTLIECITYRNYGHFEGDAQTYKTGR
+EKEEHTEERDAITLFEKYALSNNLLTEEAIQTVRHEVEQSVDRAVDFANASDYPQPEELLTDVYVSYDH
+EGRNG";
my $count;
print map $_ . (++$count % 5 ? " " : "\n"), unpack "(A10)*", $string;
'
MKTVEQTSPT MTSEKARWIY QKMVEIRMFE DRVHDIFSKG EIPGFVHLYA
GEEAIAVGLC AHLDHNDYIT STHRGHGHCI AKGCELDGMM AEIYGKSTGL
CKGKGGSMHI ADLDRGMLGA NGIVGGGFTL AAGAALTAKF KQTGGVAVCF
FGDGANNQGT FHEGINLAAI WDLPVVFVAE NNGYGEATPF HYASACEQIT
DRAKGYNIPG VKVDGKDVVA VYEVAREAVE RARRGEGPTL IECITYRNYG
HFEGDAQTYK TGREKEEHTE ERDAITLFEK YALSNNLLTE EAIQTVRHEV
EQSVDRAVDF ANASDYPQPE ELLTDVYVSY DHEGRNG
[download]

$ perl -le'
my $string = "MKTVEQTSPTMTSEKARWIYQKMVEIRMFEDRVHDIFSKGEIPGFVHLYAGEEAIA
+VGLCAHLDHNDYITSTHRGHGHCIAKGCELDGMMAEIYGKSTGLCKGKGGSMHIADLDRGMLGANGIVG
+GGFTLAAGAALTAKFKQTGGVAVCFFGDGANNQGTFHEGINLAAIWDLPVVFVAENNGYGEATPFHYAS
+ACEQITDRAKGYNIPGVKVDGKDVVAVYEVAREAVERARRGEGPTLIECITYRNYGHFEGDAQTYKTGR
+EKEEHTEERDAITLFEKYALSNNLLTEEAIQTVRHEVEQSVDRAVDFANASDYPQPEELLTDVYVSYDH
+EGRNG";
my $count;
$string =~ s/(?<=\G.{10})/ ++$count % 5 ? " " : "\n" /eg;
print $string;
'
MKTVEQTSPT MTSEKARWIY QKMVEIRMFE DRVHDIFSKG EIPGFVHLYA
GEEAIAVGLC AHLDHNDYIT STHRGHGHCI AKGCELDGMM AEIYGKSTGL
CKGKGGSMHI ADLDRGMLGA NGIVGGGFTL AAGAALTAKF KQTGGVAVCF
FGDGANNQGT FHEGINLAAI WDLPVVFVAE NNGYGEATPF HYASACEQIT
DRAKGYNIPG VKVDGKDVVA VYEVAREAVE RARRGEGPTL IECITYRNYG
HFEGDAQTYK TGREKEEHTE ERDAITLFEK YALSNNLLTE EAIQTVRHEV
EQSVDRAVDF ANASDYPQPE ELLTDVYVSY DHEGRNG
[download]