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Chris Fields | 1 Apr 2008 01:58
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Re: Bio::SeqIO - Error in ID value collection

The parser no longer has this line; it has been updated to work with  
both old and new format EMBL.  You might want to try updating from  
Subversion or install the nightly build.

http://bioperl.org/DIST/nightly_builds/

chris

On Mar 31, 2008, at 9:35 AM, Damien Pradel wrote:
> Hello,
>
> I use the SeqIO module in order to  parse EMBL files.
> Unfortunately I got a problem: the ID was not recognised because  
> instead of
> the ID value  I get the answer "unknown_id" ...
>
> So to solve this problem I have modified the file embl.pm located in
> directory SeqIO at the line 189 as follow :
>
> if( $line =~ /^ID\s+(\S+)\s+\S+\;\s+([^;]+)\;\s+(\S+)\;/ ) {
>       ($name,$mol,$div) = ($1,$2,$3);
>   }
>   unless( defined $name && length($name) ) {
>       $name = "unknown_id";
>   }
>
> in :
> if( $line =~ /^ID\s+(.+?)\;\s+([^;]+)\;\s+(\S+)\;/ ) {
>       ($name,$mol,$div) = ($1,$2,$3);
>   }
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Bánk Beszteri | 1 Apr 2008 14:31
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Indexing large databases / BioSQL

Dear list,

we have recently started to try to find a solution for indexing large 
sequence databases / flat files for a java project, and because we ran 
into problems using biojava, and because both the OBDA and BioSQL ways 
seem to be compatible across bio~ projects, we also started to 
experiment with bioperl. It looks like this should work fine, but we had 
a couple of problems here, too. Perhaps some of you can give me hint 
what we are doing wrong!

The first thing we tried was to use Bio::DB::Flat for indexing a TrEMBL 
flat file (~ 12 GB); but it seems we haven´t got a machine with enough 
memory to be able to handle this. (Perhaps you would be using the "bdb" 
style index in such a case in bioperl, but this apparently doesn´t work 
with biojava, so we had to stick with "flat"). So next we started to 
test BioSQL, by trying to load just Swissprot in a MySQL DB first, like:

load_seqdatabase.pl --host mysql.awi.de --dbname biosql2 --dbuser xyz 
--dbpass abc --driver mysql --namespace uniprot_sprot --format swiss 
uniprot_sprot.dat

Here we get an error message

###########################################

Loading /biodb/spinkern/uniprot_sprot.dat ...
Could not store Q6DAH5:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp. 
atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium
(Continue reading)

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Chris Fields | 2 Apr 2008 02:45
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quick update on bioperl nightly builds

I'm simplifying the nightly build archive names (removing svn revision  
# and date) in case anyone needs to update bioperl-live/run/db/network  
on a regular basis (read: GBrowse installations).  When I have time  
I'll start working on automated builds, which will require some extra  
work with Module::Build and Build.PL.

chris

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Jinyan Huang | 2 Apr 2008 04:14
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How to make a network graphic using my genes in pathways?

I have 20 pathways. My interesting genes are in these pathways. There
are some genes overlaps in these pathways. How can I make a graphic
network using these genes? It means connecting these pathways through
these overlap genes. What kind of software can I use?

Thank you very much in advance.

--

-- 
Best regards,
Jinyan Huang (ekeen)
School of Life Sciences and Technology, 1302 Room
Tongji University
Siping Road 1239, Shanghai 200092
P.R. China
Tel :0086-21-65981041
Msn: hiekeen <at> hotmail.com
eMail: hiekeen <at> gmail.com
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Hilmar Lapp | 2 Apr 2008 04:30
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Re: Indexing large databases / BioSQL


On Apr 1, 2008, at 8:31 AM, Bánk Beszteri wrote:
> [...] So next we started to test BioSQL, by trying to load just  
> Swissprot in a MySQL DB first, like:
>
> load_seqdatabase.pl --host mysql.awi.de --dbname biosql2 --dbuser  
> xyz --dbpass abc --driver mysql --namespace uniprot_sprot --format  
> swiss uniprot_sprot.dat
>
> Here we get an error message
>
> ###########################################
>
> Loading /biodb/spinkern/uniprot_sprot.dat ...
> Could not store Q6DAH5:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: The supplied lineage does not start near 'Erwinia carotovora  
> subsp. atroseptica' (I was supplied 'Erwinia carotovora subsp. |  
> Pectobacterium | Enterobacteriaceae | Enterobacteriales |  
> Gammaproteobacteria | Proteobacteria | Bacteria')
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /biodb/spinkern/bioperl-1.5/ 
> bioperl-1.5.2_102/Bio/Root/Root.pm:359
> STACK: Bio::Species::classification /biodb/spinkern/bioperl-1.5/ 
> bioperl-1.5.2_102/Bio/Species.pm:174
> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /biodb/ 
> spinkern/bioperl-db-1.5.2_100/Bio/DB/Persistent/PersistentObject.pm: 
> 552
> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /biodb/ 
> spinkern/bioperl-db-1.5.2_100/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
(Continue reading)

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Hilmar Lapp | 2 Apr 2008 04:38
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Re: Very basic implementation of GenBank XML SeqIO module

Ryan - do you not have a committer account?

I do agree with Chris on the test. Modules w/o tests tend to become  
'pseudogenized.'

	-hilmar

On Mar 31, 2008, at 3:31 PM, Ryan Golhar wrote:
> I have a (very) basic SAX implementation of a SeqIO module to parse  
> GenBank XML records.  Right now, it only reads in basic information  
> regarding the sequence and the sequence itself.
>
> It does not yet parse the features table.  Should I submit it to be  
> included in bioperl or wait until I implement more for the features  
> table?  I'm not sure when I'll get around to it though
>
> Ryan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================
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Scott Cain | 2 Apr 2008 05:12
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Re: [Bioperl-l] quick update on bioperl nightly builds

Hi Chris,

The tarball is currently (Apr 1) being built in a tmp directory, so that
the extracted tarball is ./tmp/bioperl-live/.  Is that intended?

Thanks,
Scott

On Tue, 2008-04-01 at 19:45 -0500, Chris Fields wrote:
> I'm simplifying the nightly build archive names (removing svn revision  
> # and date) in case anyone needs to update bioperl-live/run/db/network  
> on a regular basis (read: GBrowse installations).  When I have time  
> I'll start working on automated builds, which will require some extra  
> work with Module::Build and Build.PL.
> 
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain@...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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Chris Fields | 2 Apr 2008 05:59
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Re: [Bioperl-l] quick update on bioperl nightly builds

Nope, that isn't intended.  I fixed it and reran it manually, so it  
should be fine now (note I didn't update the log file; the next cron  
run will catch that).

I may toy around with your recent passthrough flag addition to try  
getting automated PPM's up and running.

chris

On Apr 1, 2008, at 10:12 PM, Scott Cain wrote:

> Hi Chris,
>
> The tarball is currently (Apr 1) being built in a tmp directory, so  
> that
> the extracted tarball is ./tmp/bioperl-live/.  Is that intended?
>
> Thanks,
> Scott
>
> On Tue, 2008-04-01 at 19:45 -0500, Chris Fields wrote:
>> I'm simplifying the nightly build archive names (removing svn  
>> revision
>> # and date) in case anyone needs to update bioperl-live/run/db/ 
>> network
>> on a regular basis (read: GBrowse installations).  When I have time
>> I'll start working on automated builds, which will require some extra
>> work with Module::Build and Build.PL.
>>
>> chris
(Continue reading)

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Sean Davis | 2 Apr 2008 13:33
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Re: How to make a network graphic using my genes in pathways?

On Tue, Apr 1, 2008 at 10:14 PM, Jinyan Huang <hiekeen <at> gmail.com> wrote:
> I have 20 pathways. My interesting genes are in these pathways. There
>  are some genes overlaps in these pathways. How can I make a graphic
>  network using these genes? It means connecting these pathways through
>  these overlap genes. What kind of software can I use?

R/Bioconductor has tools for working with graphs and pathways.
Cytoscape is another open-source graphical solution.  Ingenuity is, of
course, not free.  If you are looking at a perl solution, you can look
at the various graph modules and their integration with the Graphviz
libraries.

SEan
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Scott Cain | 2 Apr 2008 14:28
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Re: [Gmod-gbrowse] quick update on bioperl nightly builds

Hi Chris,

(trimmed out gbrowse mailing list since this is just bioperl business)

Speaking of the pass through stuff, Sendu mentioned that I stomped on
some changes to Build.PL that you and he did when I committed that
change, so it should be rolled back.  Is there a good (svn) way to do
that?  Or should I just copy the contents of the old (good) Build.PL
into a fresh file in my checkout and commit it?

Thanks,
Scott

On Tue, 2008-04-01 at 22:59 -0500, Chris Fields wrote:
> Nope, that isn't intended.  I fixed it and reran it manually, so it  
> should be fine now (note I didn't update the log file; the next cron  
> run will catch that).
> 
> I may toy around with your recent passthrough flag addition to try  
> getting automated PPM's up and running.
> 
> chris
> 
> On Apr 1, 2008, at 10:12 PM, Scott Cain wrote:
> 
> > Hi Chris,
> >
> > The tarball is currently (Apr 1) being built in a tmp directory, so  
> > that
> > the extracted tarball is ./tmp/bioperl-live/.  Is that intended?
(Continue reading)

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Gmane