[Bioperl-l] HTML writers

[nkuipers]

Thanks Brian,

I had a feeling I would have to roll my own.  Perhaps when I am intimately 
familiar with the guts of bioperl I will contribute some format-to-format HTML 
writers.

Hilmar, you mentioned in your response to my earlier question about CGI and 
SeqIO filehandles that you didn't think the code would work.  Maybe it 
shouldn't have, but it did.  The autoflush $fh 1 suggested by Jamie was all I 
needed to get the html interspersed with the sequence object information 
properly, but even before that, my original code printed everything to the 
same destination, if not the same handle (seqio object made with the same 
filename as that pointed to by the separate $fh variable).  I mention it as a 
matter of semantic interest.

Thanks everyone,

Nathanael


>===== Original Message From "Brian Osborne" <brian_osborne at cognia.com> =====
>Nathanael,
>
>I don't think there's a module tailor-made for this, no, but you could make
>a script in a few minutes. Get the HTML in question, replace each relevant
>section with a variable, read the fasta file into a Seq object, use the
>appropriate Bio::Seq method to write to the appropriate variable. Done.
>Well, I lied, you'd have to spend a few more minutes formatting some
>sections if you wanted it picture-perfect.
>
>There's a little section at the end of the Bio::Seq documentation that talks
>about how fasta "fields" map to Genbank fields:
>
>http://doc.bioperl.org/releases/bioperl-1.2/Bio/Seq.html
>
>Brian O.
>
>-----Original Message-----
>From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
>Behalf Of nkuipers
>Sent: Friday, February 07, 2003 2:44 PM
>To: bioperl-l at bioperl.org
>Subject: [Bioperl-l] HTML writers
>
>Are there bioperl modules that will convert, say, a fasta flat file into a
>genbank-formatted .html file?  I see the Bio::Tools::Blast::HTML and
>Bio::SearchIO::Writer::HTMLResultWriter namespaces, but these don't seem to
>me
>to deal with a straight fasta flat file (not generated by a FASTA search).
>Any ideas?
>
>Thanks,
>
>Nathanael
>
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