[Bioperl-l] Tracking database dates in BLAST

[Wiepert, Mathieu]

Hi,

I was only going to add one, not two methods?  And this "Posted date" is not in the XML spec output I notice, so I am not really sure what the proper way to make the data available is.

I didn't see any other data that was not entered like 
 (from blast.pm)

$self->element({'Name' => 'Statistics_lambda',
	       'Data' => $lambda});

So without XML slot, what do you suggest.

And of course you are correct that not all results have this, I just wasn't sure where to place it, if at all (any suggs welcome)

-Mat

-----Original Message-----
From: Jason Stajich [mailto:jason at cgt.mc.duke.edu]
Sent: Wednesday, March 19, 2003 12:20 PM
To: Wiepert, Mathieu
Cc: Bioperl
Subject: RE: [Bioperl-l] Tracking database dates in BLAST


Mat-

I think it should be added the way the rest of the parameters and
statistics meta-data methods are available.  If we want an additional
meta-data accessor other than these two that is fine too, but let's not
add a method just for this since it is not data is available from all
search programs and plus I am sure there are other fields people will
still want to slot in.

-jason



On Wed, 19 Mar 2003, Wiepert, Mathieu wrote:
Hi,

> hi,
>
> I am going to assume that you are talking about the posted date, at the bottom of the blast file?  If that's the case, and that data is always there, I'd be willing to add that bit of data into the interface and object that parses?  Should that be the ResultI interface?  I am assuming it could be retrieved like
>
> my $io = new Bio::SearchIO(-format => 'blast',
>  			       -file   => $ARGV[0]);
> my $result = $io->next_result;
> my $desc = $result->query_description();
> my $dbname = $result->database_name();
> my $dbdate = $result->database_posted_date();#or database_date?
>
> -Mat
>
>
> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: Wednesday, March 19, 2003 11:03 AM
> To: Andy Nunberg; Bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Tracking database dates in BLAST
>
>
> Andy,
>
> > I was wondering if anyone has added a method that allows to capture the
> > date a database is created in Bio::SearchIO::blast ?
>
> No, I don't think so, see http://www.bioperl.org/HOWTOs/html/SearchIO.html
> for a list of available methods. This HOWTO also discusses the event-based
> parsing that Jason and Steve use in SearchIO, perhaps you could figure out
> how to capture this string. Check out SearchIO/blast.pm, you will see how
> the event-based approach ties in with the actual work done with the regular
> expressions.
>
> Brian O.
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
> Behalf Of Andy Nunberg
> Sent: Wednesday, March 19, 2003 11:33 AM
> To: Bioperl-l at bioperl.org
> Subject: [Bioperl-l] Tracking database dates in BLAST
>
> Hi,
> I was wondering if anyone has added a method that allows to capture the
> date a database is created in Bio::SearchIO::blast ?
>
> I am interested in tracking this information.  I have looked at the
> Bio::SearchIO::blast->next_result to see how the parsing is done, but I am
> not clear on how to use the methods in it (eg. start_document, element
> etc..) or if this is even necessary to use them to do what I want to
> accomplish.
>
> Andy
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC
> (314) 615-6989
> http://www.oriongenomics.com
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu