Re: Proposal for bio-perl updates: ACE assembly file

Hi Jordan,

I have been doing some work on Contig::Assembly myself recently, and 
have also been in touch with the author (Robson) about it. Perhaps the 
best thing would be for the three of us to have a chat about this 
object, try to revamp it a little with our improvements, and then 
Robson or I can check it in?

regards,

Elia

On Feb 28, 2005, at 5:05 PM, Jordan Swanson wrote:

> On Monday 14 February 2005 12:05 pm, Jordan Swanson wrote:
>> Hi,
>> I am new to bioperl, but I have a proposal for updating bioperl with 
>> some
>> of the code I have been using.
>>
>> Bioperl packages currently exist that open ACE assembly files (output 
>> by
>> phrap/cap3, and other assembly program).  However, the current code 
>> brings
>> in the entire file in one call:
>>
>> my $assembly_in =
>> 	 Bio::Assembly::IO->new(-file=>"input.ace",
>> 						-format=>'ace');
>>

Re: Proposal for bio-perl updates: ACE assembly file

On Tuesday 01 March 2005 05:51 am, Elia Stupka wrote:
> Hi Jordan,
>
> I have been doing some work on Contig::Assembly myself recently, and
> have also been in touch with the author (Robson) about it. Perhaps the
> best thing would be for the three of us to have a chat about this
> object, try to revamp it a little with our improvements, and then
> Robson or I can check it in?

Good idea,  you and Robson can expect a copy of my changes very soon.

--

-- 
Jordan M Swanson   
Department of Ecology, Evolution, and Organismal Biology 
431 Bessey Hall 
Iowa State University 
Ames, IA 50011 
Lab 515 294-7098 
FAX: 515-294-1337 

Re: which one and how to configure(blastall)

Hi Yanfeng,

Try this:
(I make the assumption, that your blast installation is in 
/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10).

Create a file named   .ncbirc (don't forget the little dot)  in 
/home/yanfeng and write the following in this file:

    [NCBI]
    DATA="/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/data"

save file.

In the data dir, BLAST will find the BLOSSUM tables.

In your blast installation dir you will find also db dir. That's a good 
place to store your blast databases.

Set the environment variables in your .bashrc  (.profile, .cshrc...... - 
depends on your shell) . I know it's trivial, but..... .

something like [bash]:

<>BLASTDIR=/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10
<>export BLASTDIR

<>BLASTDB=/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/db
<>export BLASTDB

blastall & StandAloneBlast

Hi all,

I'm yet again being faced with a mysterious crash in blastall and Bioperl 
that has been occuring for the past year.  I'm receiving more reports from 
people around the world using our software also experiencing this problem, 
and the only answer I once received about the problem was, "That shouldn't 
be possible."

Anyhow, the error occurs when blastall is called from StandAloneBlast.pm, 
Blast returns with a -1 error code which causes the Bioperl module to 
throw an exception.  We've had reports of this occurring on multiple Linux 
distributions as well as on Solaris and OS X.  But it doesn't happen on 
all machine even if they're running the same distribution.

The crash output is below....

Fatal error:
------------- EXCEPTION  -------------
MSG: blastall call crashed: -1 /usr/local/blast/blastall -p  blastp  -d
"/usr/local/psort/conf/analysis/sclblast/gramneg/sclblast"  -i
/var/tmp/6m0QxSirC3  -e  1e-09  -o  /var/tmp/AKCDNMCTyo  -F  F

STACK Bio::Tools::Run::StandAloneBlast::_runblast
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:751
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:698
STACK Bio::Tools::Run::StandAloneBlast::blastall
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:553
STACK Bio::Tools::Run::SCLBlast::blast
/usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/SCLBlast.pm:135

Bio::LiveSeq::Transcript query from new bioperl user

This is a request for help from a *very* new bioperl user. IM also 
pretty new to perl....

I want to use the Bio::LiveSeq::Transcript->new method to make a 
transcript object from an .embl file.

I then want to use the $frame = $transcript->frame($label) method so 
that I can trim sub-sections of the transcript to include only complete 
codons.

So, in other words, I want to collect subsets of a transcript 
(coordinates that I have defined earlier), and then trim those 
coordinates to the nearest complete codons. And the get the sequence of 
those coordinates.

____________________________
Daniel Jeffares
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SA, UK
Phone: +44(0)1223 834244 x 7297
____________________________

_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l

Re: blastall & StandAloneBlast

Could you send the output you get when you comment the throw and print 
out the errors you mention below?

Elia

On 2 Mar 2005, at 19:36, Matthew Laird wrote:

> When I've
> editted the error message being thrown to give more details, perl says 
> the
> error is related to a process not being able to be created, which is 
> even
> weirder.

Re: blastall & StandAloneBlast

When I comment out the throw there is no output because the program 
executes correctly.  blastall runs and returns the results through 
bioperl.  That's the mysterious part of this.

On Wed, 2 Mar 2005, Elia Stupka wrote:

> Could you send the output you get when you comment the throw and print 
> out the errors you mention below?
> 
> Elia
> 
> On 2 Mar 2005, at 19:36, Matthew Laird wrote:
> 
> > When I've
> > editted the error message being thrown to give more details, perl says 
> > the
> > error is related to a process not being able to be created, which is 
> > even
> > weirder.
> 
> 

--

-- 
Matthew Laird
SysAdmin/Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University

Re: blastall & StandAloneBlast

Sorry, wrote my answer badly, I meant when you mentioned that printing 
more details about the error it gave you something weird about process 
not being able to be created:

> editted the error message being thrown to give more details, perl says 
>  the error is related to a process not being able to be created, which 
> is  even weirder.
>

Elia

Re: blastall & StandAloneBlast

Alas no.  I no longer have any machines around I had to do the hack on.  I 
just tried to install it on two other machines and it sadly ran fine.... 
I'm reluctant to harass any of the users who have emailed us and ask them 
to intentionally "break" their install (by uncommenting that line) to help 
us test this.

Anyhow, I had just added $! to the error message and it said something 
along the lines of "Process can not be created."

On Wed, 2 Mar 2005, Elia Stupka wrote:

> Sorry, wrote my answer badly, I meant when you mentioned that printing 
> more details about the error it gave you something weird about process 
> not being able to be created:
> 
> > editted the error message being thrown to give more details, perl says 
> >  the error is related to a process not being able to be created, which 
> > is  even weirder.
> >
> 
> Elia
> 
> 

--

-- 
Matthew Laird
SysAdmin/Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University

Re: Bio::LiveSeq::Transcript query from new bioperl user

Daniel,

While LiveSeq can be used for this, there is quite a lot of overhead in 
creating those objects. If you are going to apply this in a highthroughput
pipeline, I recommend you retrieve the CDS feature from the standard 
SeqIO-produced sequence object and determine the frame yourself.

Let me know in more detail what you want to do and I'll help you.

	-Heikki

On Wednesday 02 March 2005 13:27, Daniel Jeffares wrote:
> This is a request for help from a *very* new bioperl user. IM also
> pretty new to perl....
>
> I want to use the Bio::LiveSeq::Transcript->new method to make a
> transcript object from an .embl file.
>
> I then want to use the $frame = $transcript->frame($label) method so
> that I can trim sub-sections of the transcript to include only complete
> codons.
>
> So, in other words, I want to collect subsets of a transcript
> (coordinates that I have defined earlier), and then trim those
> coordinates to the nearest complete codons. And the get the sequence of
> those coordinates.
>
> ____________________________
> Daniel Jeffares
> Wellcome Trust Sanger Institute