[Bioperl-l] seq to fasta

[stephan rosecker]

Hi,
thx Hilmar but no luck for me.
I made somthing wrong...?


sub test($)
{
         use Bio::SeqIO;
         use IO::String;
         my $io = IO::String->new();
         my $out = Bio::SeqIO->new(-fh => ">$io",
                                  -format => 'Fasta');
         $out->write_seq($_);
         my $erg = $io;
}

result:
Can't use string (">IO::String=GLOB(0x106c2018)") as a symbol ref while 
"strict refs" in use at 
/xprog/perl/perl-5.9.1_inst/lib/site_perl/5.9.1/IP27-irix/Bio/Root/IO.pm 
line 407.

sorry... i'm a newbie -

regards,
stephan




Hilmar Lapp wrote:
 > Use IO::String to create a stream that writes to a string, pass it to
 > SeqIO using -fh, call $out->write_seq($seq), and then print the string
 > used for creating the stream.
 >
 >     -hilmar
 >
 > On Sunday, May 23, 2004, at 03:17  PM, stephan rosecker wrote:
 >
 >> Hi,
 >> is it possible to get the fasta format from a seqobject-sequence in a
 >> variable without using filhandles like below ?
 >>
 >> use Bio::SeqIO;
 >>   $in  = Bio::SeqIO->new(-file => "inputfilename",
 >>                          -format => 'EMBL');
 >>   $out = Bio::SeqIO->new(-file => ">outputfilename",
 >>                          -format => 'Fasta');
 >>   while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
 >>
 >> e.g:
 >> I've a seqobject ($seq).
 >> and this is what i want:
 >>
 >> my $fastavar = $seq->seq_fastaformat();
 >> print $fastavar;
 >>
 >> result:
 >> >sp|P32234|128U_DROME GTP-binding protein 128UP - Drosophila
 >> melanogaster (Fruit fly).
 >> MITILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELISPKGGGGGTGEAGFEVA
 >> KTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPG
 >> IIEGAKDGKGRGRQVIAVARTCNLIFMVLDCLKPLGHKKLLEHELEGFGIRLNKKPPNIY
 >> YKRKDKGGINLNSMVPQSELDTDLVKTILSEYKIHNADITLRYDATSDDLIDVIEGNRIY
 >> IPCIYLLNKIDQISIEELDVIYKIPHCVPISAHHHWNFDDLLELMWEYLRLQRIYTKPKG
 >> QLPDYNSPVVLHNERTSIEDFCNKLHRSIAKEFKYALVWGSSVKHQPQKVGIEHVLNDED
 >> VVQIVKKV
 >>
 >> regards,
 >> stephan
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 >>