[Biophp-dev] Little suggestion for fasta.inc.php

[biophp-dev@bioinformatics.org]

Hello biophp group,

I am starting the embl export module.
I would like to do a little suggestion concerning fasta.inc.php

I think it would be useful to replace code1 by code2 to treat the case =
of fasta sequence from NCBI in order to get more information at once =
from the >defline

############## start code 1################
function fetchNext()
    {
        $record=3DArray(); //for returning results
        if($this->next_label) {
            list($id,$sequence)=3D$this->findNextLabel();
            $record['id']=3D$id;
            $record['sequence']=3D$sequence;
            return $record;
        }
        else {
            //no more records in file
            return false;
        }
    }


############## end code 1################

############## start code 2################
function fetchNext()
    {
        $record=3DArray(); //for returning results
        if($this->next_label) {
            list($id,$sequence)=3D$this->findNextLabel();
            //treat the Defline used at NCBI eg=20
            //>gi|42794768|ref|NM_002576.3| Homo sapiens =
p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) (PAK1), mRNA
            if(ereg("^gi", $id)) {
            $id =3D substr($id, 3); //take off "gi|"
            list($id, $db, $accession_version, $definition) =3D =
explode("|", $id);
            list($accession, $version) =3D explode(".", =
$accession_version);
            $record['ncbi_gi_id']   =3D$id;
            $record['id']           =3D$accession;
            $record['accession']    =3D$accession;
            $record['version']      =3D$version;
            $record['definition']   =3D$definition;
            }
            else {
            $record['id']=3D$id;
            }
            $record['sequence']=3D$sequence;
            return $record;
        }
        else {
            //no more records in file
            return false;
        }
    }


############## end code 2################


By the way how is it possible to append some code I think usefull for =
other biophp addicted.
Thanks in advance.
By the way what is the officiel website of BIOPHP ?

Thanks in advance for any response.

regards,

Fred
-----Message d'origine-----
De : biophp-dev-admin@bioinformatics.org
[mailto:biophp-dev-admin@bioinformatics.org]De la part de S Clark
Envoy=E9 : jeudi 1 juillet 2004 18:51
=C0 : biophp-dev@bioinformatics.org
Objet : Re: [Biophp-dev] Question


In order to add code to the CVS tree at bioinformatics.org, you'll need
a bioinformatics.org login name, and I'll need to add it to the
developers list...and that's about it.  (The instructions for CVS itself
are on the bioinformatics.org website).  If you already have a
bioinformatics.org login (or as soon as you've got one) let me know and
I'll add you to the developer list.

We DO have import and export frameworks ready for initial use, but the
only export module currently written is a simple FASTA example.  If you
had time to add a Genbank and/or embl format module in the same style to
add to the export section that'd be very helpful!  Take a look at=20
seqIOExport.inc.php and exporters/export_fasta.inc.php - that should
(hopefully) show how an "export_genbank.inc.php" class should be
structured (comments and suggestions, as always, are welcome...)
The current code is (for the moment) actually residing in the "genephp"
section.  Reorganization under the biophp section should happen Real =
Soon Now.=20
(The whole "two different-but-cross-pollinating projects with the same =
name"
thing IS a bit confusing...)

We may be really quiet right now (probably a combination of work and =
school=20
hitting us all again - that's MY excuse, anyway) but we're not dead =
yet...

Thanks!

Sean

P.S. I'm not sure about getting 24 extra hours in the day - I have a =
sneaking
suspicion that the work day would just expand to compensate.=20
That kilo of that pure laboratory-grade Caffeine in the chemical supply
catalogs looks more appealing all the time...

On Thursday 01 July 2004 01:30 am, Frederic.Fleche@aventis.com wrote:
> Hello ,
> I was busy during the last months so my Locuslink file is still under
> construction, by the way, what is the way if I want to append my code =
to
> this directory :
>
>
> http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/
> My question is : Does any one have a biophp module to automatically =
convert
> a fasta file into an embl or genbank file. Actually I use Bioperl to =
do
> that but I would be glad to do all in PHP. If it doesn't exist a =
solution
> yet I will try to take the time to build it. Ha It would be great if =
the
> days were 24 hours longer !!!!!!!
>
>
> Thanks in advance
> Fred
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