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Brian Osborne | 1 Nov 03:31
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Re: Bio::SeqIO::scf header/comments handling

Nancy,

It looks like a good place to start would be the get_header() and
_get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that
the author, at some point, wanted get_header to return meaningful
information but stepping through the test shows it returning a lot of UNDEF.
Now I don't know if this is due to the method or the source SCF file, but
you might be able to get these methods to work yourself.

But to answer your questions, yes, it certainly sounds reasonable that these
values would be extracted by Bio::SeqIO::scf.

Brian O.

On 10/31/06 3:51 PM, "Nancy Hansen" <nhansen <at> nhgri.nih.gov> wrote:

> 
> Hello,
> 
> As sequencing centers begin to deposit trace data from "Medical
> Sequencing" projects into the public archives, there is now the need to
> "anonymize" sequence trace files by removing embedded information which
> might be used to identify the individual who was the original source of
> the DNA being sequenced.
> 
> I was hoping I might be able to use Bio::SeqIO to manipulate the
> comments contained in an SCF-formatted trace file, but I'm finding that
> Bio::SeqIO/Bio::Seq::SequenceTrace doesn't seem to store this information.
> Since SCF is a widely-accepted standard for trace files, would it be
> reasonable to include fields like "scf_comments" and "scf_header" in a
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Huang Yi | 1 Nov 09:25
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Re: bioperl1.5 and GD2.35 - solved


The problem was solved.

I re-emerged gd-2.0.33 with png USE flag.

Thanks again!

Huang Yi

-----Original Message-----
From: bioperl-l-bounces <at> lists.open-bio.org
[mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of Kevin Brown
Sent: Tuesday, October 31, 2006 11:35 PM
To: bioperl-l <at> lists.open-bio.org
Subject: Re: [Bioperl-l] bioperl1.5 and GD2.35

Not really a Bioperl issue per se, but sounds like when you had Gentoo
emerge GD it didn't include libpng and so didn't build the needed parts
to create PNG type graphics. 

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org 
> [mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of Huang Yi
> Sent: Monday, October 30, 2006 10:46 PM
> To: bioperl-l <at> lists.open-bio.org
> Subject: [Bioperl-l] bioperl1.5 and GD2.35
> 
> Hi,
> 
>
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Nancy Hansen | 1 Nov 14:43
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Re: Bio::SeqIO::scf header/comments handling


On Tue, 31 Oct 2006, Brian Osborne wrote:

> It looks like a good place to start would be the get_header() and
> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that
> the author, at some point, wanted get_header to return meaningful
> information but stepping through the test shows it returning a lot of UNDEF.
> Now I don't know if this is due to the method or the source SCF file, but
> you might be able to get these methods to work yourself.
>
> But to answer your questions, yes, it certainly sounds reasonable that these
> values would be extracted by Bio::SeqIO::scf.

Sounds great!  So, if I make these changes, is there someone I should run
them by before checking them into CVS?  Is Chad Matsalla still involved in
bioperl?  I've never contributed to the project, so I'm not sure how
things work...

	Thanks!
	--Nancy

*************************************
Nancy F. Hansen, PhD	nhansen <at> nhgri.nih.gov
Bioinformatics Group
NIH Intramural Sequencing Center (NISC)
5625 Fishers Lane
Rockville, MD 20852
Phone: (301) 435-1560	Fax: (301) 435-6170
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Mauricio Herrera Cuadra | 1 Nov 15:30
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Re: Bio::SeqIO::scf header/comments handling

The usual way is to send your modifications as an 'enhancement' through 
the Bugzilla system (please add your patches as attachments after 
creating the report, not into the description field):

http://bugzilla.open-bio.org/

Thanks for contributing!

Regards,
Mauricio.

Nancy Hansen wrote:
> On Tue, 31 Oct 2006, Brian Osborne wrote:
> 
>> It looks like a good place to start would be the get_header() and
>> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that
>> the author, at some point, wanted get_header to return meaningful
>> information but stepping through the test shows it returning a lot of UNDEF.
>> Now I don't know if this is due to the method or the source SCF file, but
>> you might be able to get these methods to work yourself.
>>
>> But to answer your questions, yes, it certainly sounds reasonable that these
>> values would be extracted by Bio::SeqIO::scf.
> 
> Sounds great!  So, if I make these changes, is there someone I should run
> them by before checking them into CVS?  Is Chad Matsalla still involved in
> bioperl?  I've never contributed to the project, so I'm not sure how
> things work...
> 
> 	Thanks!
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Chris Fields | 1 Nov 15:39
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Re: Bio::SeqIO::scf header/comments handling

> On Tue, 31 Oct 2006, Brian Osborne wrote:
> 
>> It looks like a good place to start would be the get_header() and
>> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can
>> see that the author, at some point, wanted get_header to return
>> meaningful information but stepping through the test shows it
>> returning a lot of UNDEF. Now I don't know if this is due to the
>> method or the source SCF file, but you might be able to get these
>> methods to work yourself. 
>> 
>> But to answer your questions, yes, it certainly sounds reasonable
>> that these values would be extracted by Bio::SeqIO::scf.
> 
> Sounds great!  So, if I make these changes, is there someone
> I should run them by before checking them into CVS?  Is Chad
> Matsalla still involved in bioperl?  I've never contributed
> to the project, so I'm not sure how things work...
> 
> 	Thanks!
> 	--Nancy

You can check them into Bugzilla as a patch to a bug:

http://bugzilla.open-bio.org/

There is a HOWTO for patch submission here:

http://www.bioperl.org/wiki/HOWTO:SubmitPatch

You could also send them to Brian or me.  Bugzilla is probably your best bet
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Brian Osborne | 1 Nov 14:00
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Re: Bio::SeqIO::scf header/comments handling

Nancy,

I suggest doing this through Bugzilla, http://bugzilla.open-bio.org. First
add your proposal as a bug or as an enhancement, sounds like it could be
either but I'd say it doesn't matter. Then contribute patches to the "bug"
as you work, some one will apply them. Also add tests to t/scf.t, if you're
working on scf.pm. Thank you in advance for your contributions. As for Chad,
I have no idea but strictly speaking no one "owns" a module in Bioperl.

Brian O.

On 11/1/06 9:43 AM, "Nancy Hansen" <nhansen <at> nhgri.nih.gov> wrote:

> Sounds great!  So, if I make these changes, is there someone I should run
> them by before checking them into CVS?  Is Chad Matsalla still involved in
> bioperl?  I've never contributed to the project, so I'm not sure how
> things work...
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Keith Player | 2 Nov 01:22
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Article

Sorry I didn't attach the article link originally.  You can view the full-text 
for free:

http://www.genome.org/cgi/content/abstract/12/10/1599

When I was talking about the R-tree I was talking about the current 
implementation.  

I should point out that I didn't actually try the perl module directly but 
implemented the binning schema straight in mysql.  I found that by using the 
SQL I mentioned previously the database performed better compared to using the 
binning schema, I assume because of less disk seeks.  I tested on a dataset of 
around 30k records and another the same size as the paper.  The binning 
outperformed the queries as described in the paper, but the SQL I mentioned in 
the first post outperformed the binning schema by around a factor of 3.  

The new binning schema might make all this moot, especially if it removes 
layers so that groups/features next to each other are saved on the 
same/adjacent pages.  The only question then would be whether database 
optimization is effected by the binning.

Also does needing to know the largest length of a group/feature make the SQL 
statement I created impractical?
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Sean O'Keeffe | 1 Nov 17:28
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Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336.

Hi,
I am currently in the process of trying testing Gbrowse with the
(relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple
of teething problems, just wondering if anyone else had encountered
the message above. Any insight appreciated.
Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had
to be copied into the lowercase 'dbi' from its original DBI form -
don't know if this was a previously reported bug.

Thanks,
Sean.
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Eugene Bolotin | 2 Nov 01:15
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Check sequence format, question

Dear bioperl mailing list,
I trying to get sequence from a file using Bio::SeqIO, before I do anything,
I want to make sure that the file is in a correct Fasta sequence format. I
want it to spit out an error message if it is in any other format.
What is the easiest way to do it?
Thanks,
Eugene Bolotin
Sladek Lab.
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Chris Fields | 2 Nov 05:28
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Re: Check sequence format, question

On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote:

> Dear bioperl mailing list,
> I trying to get sequence from a file using Bio::SeqIO, before I do  
> anything,
> I want to make sure that the file is in a correct Fasta sequence  
> format. I
> want it to spit out an error message if it is in any other format.
> What is the easiest way to do it?
> Thanks,
> Eugene Bolotin
> Sladek Lab.

There is no formal FASTA definition that is universally accepted  
beyond having the first line start with '>' and an optional  
description, with the sequence in subsequent lines.

http://www.bioperl.org/wiki/FASTA_sequence_format

Bio::SeqIO isn't currently set up to validate sequence formats  
directly, but you could try preparsing the data using  
Bio::Tools::GuessSeqFormat.

Chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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