[Bioperl-l] Tracking database dates in BLAST

[Wiepert, Mathieu]

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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