[Bioperl-l] seq to fasta

[Hilmar Lapp]

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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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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