Chris Fields | 1 Mar 03:41 2006
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WGS sequences through Bio::DB::GenBank

I know that a recent post showed that you could retrieve CONTIG sequences
from GenBank files fairly easily:

http://bioperl.org/pipermail/bioperl-l/2006-February/020891.html

I'm driving myself a bit buggy looking for this, and I may be blind to it,
but can the same be done with WGS files?  I've tried Bio::DB::GenBank and a
few other Bio::DB* modules to see if it's been implemented but haven't had
any luck yet.  I may try getting around it using Bio::DB::Query::GenBank,
but just trying to find a more direct route.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 
Jon Manning | 1 Mar 16:19 2006
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pSW question- hanging tails of alignments

Hi all,

I'm using the Bio::Tools::pSW module to align two very similar 
sequences. But one is a little longer at the start than the other. 
Rather than showing this, pSW simply trims it off and it's not present 
in the resulting Bio::SimpleAlign object- a sort of BLAST-like behaviour 
I suppose, showing only aligned regions. But is there a parameter I can 
pass to allow these regions to be kept? Or am I doing something wrong.

Incidentally, the behavior is the same in dpAlign.

Thanks,

Jon Manning
Harald | 1 Mar 16:44 2006
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newbie tries StandAloneBlast and receives "cant open BLOSUM62"

Hi all.

I am a Bioinformatics Newbie and want to use BioPerl for doing BLASTs on 
a local protein-sequence file. Unfortunately something went wrong, which 
gives me the error message: "...Unable to open BLOSUM62...".

I am using Win2000 on a normal Desktop PC with 1.4 GHz AMD and 256 MB 
RAM (I know, this is not much, but my sequence database is not so big).
My perl-interpreter is from ActiveState and in the version 5.8.7 built 
for MSWin32-x86-multi-thread
BioPerl is version 1.4
Blast has version 2.2.13

(1) I have downloaded the blast distribution from 
http://www.ncbi.nlm.nih.gov/blast/download.shtml

(2) I have installed it and put the file ncbi.ini into my 
WINNT-directory, which is pointing to blast-directory/data
==============C:/WINNT/ncbi.ini========================
[NCBI]
Data="D:/BLAST/BLAST-2.2.13/data"
===================================================

(3) I downloaded a FASTA-formatted protein-sequence database file 
(ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kyva) [48MB]

(4) I used formatdb -i kyva and received the files kyva.phr, kyva.pin 
and kyva which I put into the directory, where my perl-script resides.

(5) Now I tried to BLAST this database for a sequence, I have copied out 
(Continue reading)

Chris Fields | 1 Mar 17:34 2006
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Re: newbie tries StandAloneBlast and receives "cant openBLOSUM62"

You're running a pretty old version of bioperl.  Bioperl 1.5.1 is the latest
and should work with BLAST output from v 2.2.13 (NCBI never upgraded the
formatting for netblast client and local blast, so it's text output is
exactly like v. 2.2.12; only web output has changed).  

I suggest upgrading to the latest CVS using the following instructions:

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Beyond_the_Core

Don't worry if 'nmake test' fails a number of times; it's a bit flaky with
bioperl-live.  This should install over the old version.  

If you're really wanting to stick with PPM and are especially brave, I put
up a VERY preliminary online method of making a custom PPM version of
bioperl:

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

It's a bit longish. But the nice thing about this is you get very pretty,
browsable autogenerated HTML docs from POD for all of the installed modules,
including bioperl!  New versions of PPM do this automagically. 

If installing from CVS doesn't fix it drop a line here again.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
(Continue reading)

Jason Stajich | 1 Mar 17:36 2006

Re: pSW question- hanging tails of alignments

that is actuall local alignment behavior - look into a global  
alignment like needleman-wunsch implemented in EMBOSS in the tool  
'needle'.

On Mar 1, 2006, at 10:19 AM, Jon Manning wrote:

> Hi all,
>
> I'm using the Bio::Tools::pSW module to align two very similar
> sequences. But one is a little longer at the start than the other.
> Rather than showing this, pSW simply trims it off and it's not present
> in the resulting Bio::SimpleAlign object- a sort of BLAST-like  
> behaviour
> I suppose, showing only aligned regions. But is there a parameter I  
> can
> pass to allow these regions to be kept? Or am I doing something wrong.
>
> Incidentally, the behavior is the same in dpAlign.
>
> Thanks,
>
> Jon Manning
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
(Continue reading)

Scott Cain | 2 Mar 04:26 2006

Re: Problem with bp_pg_bulk_load_gff

Hi Marco,

Please always send questions about bioperl to both the bioperl list and
the author so that the questions (and answers) can be archived.

The Postgres bulk loader tries to use a temporary directory to write
files to; it tries to use these directories in order:

  $TMPDIR (environment variables)
  $TMP
  /usr/tmp

So if you don't have either TMPDIR or TMP environment variables set, it
will try to use /usr/tmp.  So, to fix this, either set one of those
variables, or create /usr/tmp and make it world readable and writable.

Scott

On Wed, 2006-03-01 at 16:23 -0800, Marco Blanchette wrote:
> Scott--
> 
> I am trying to use the pg_bulk_load_gff.pl script you wrote without
> any success. I have PostgreSQL up and running and I can use:
> $ bp_load_gff.pl --adaptor dbi::pg  -d chr4  --create
> dmel-4-r4.2.1.gff
> to load a gff file to the chr4 PostgresSQL database.
> 
> Here is the output I get when I run your script:
> 
> $ bp_pg_bulk_load_gff.pl -d chr4 dmel-4-r4.2.1.gff 
(Continue reading)

Chris Fields | 2 Mar 05:04 2006
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Re: WGS sequences through Bio::DB::GenBank

Thanks, Brian.  I was actually typing this up when you responded.  

Okay, to answer my own question somewhat (and to confirm your answer), there
IS no direct way; efetch doesn't complete these files, so the best way is
with a query.  I'm posting this so anybody searching the mail list with the
same question will maybe find this.  The NCBI help desk basically told me to
use a query like so:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term
=AAOH00000000[accn]+AND+wgs_contig[prop]

which needs to be parsed for the individual contigs.  I tried the same query
using Bio::DB::Query::GenBank and got it to work.

As for NCBIHelper, I'll give it a look and try adding this in but it won't
be until next week.  

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

> -----Original Message-----
> From: Brian Osborne [mailto:osborne1 <at> optonline.net]
> Sent: Wednesday, March 01, 2006 9:55 PM
> To: Chris Fields
> Subject: Re: [Bioperl-l] WGS sequences through Bio::DB::GenBank
> 
> Chris,
> 
(Continue reading)

Rutger Vos | 2 Mar 09:53 2006
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Bio::Tools::Run::* extending

Hi all,

I'd like to write some more Bio::Tools::Run::* wrappers, so I'm 
wondering what the canonical approach is. Which libraries *should* I 
look at (as examples of the bioperl received wisdom and coding 
standards) and which ones *shouldn't* I look at? I'm thinking that paup, 
mrbayes and modeltest need wrappers.

Thanks!

Rutger

--

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++
Rutger Vos, PhD. candidate
Department of Biological Sciences
Simon Fraser University
8888 University Drive
Burnaby, BC, V5A1S6
Phone: 604-291-5625 
Fax: 604-291-3496
Personal site: http://www.sfu.ca/~rvosa
FAB* lab: http://www.sfu.ca/~fabstar
Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
++++++++++++++++++++++++++++++++++++++++++++++++++++
Torsten Seemann | 2 Mar 11:50 2006
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Re: newbie tries StandAloneBlast and receives "cant open BLOSUM62"

Harald,

> I am a Bioinformatics Newbie and want to use BioPerl for doing BLASTs on 
> a local protein-sequence file. Unfortunately something went wrong, which 
> gives me the error message: "...Unable to open BLOSUM62...".

> ==============C:/WINNT/ncbi.ini========================
> [NCBI]
> Data="D:/BLAST/BLAST-2.2.13/data"
> ===================================================

> [NULL_Caption] WARNING:  [000.000]  test_query: Unable to open BLOSUM62
> [NULL_Caption] WARNING:  [000.000]  test_query: BlastScoreBlkMatFill 
> returned no
> n-zero status
> [NULL_Caption] WARNING:  [000.000]  test_query: SetUpBlastSearch failed.
> 0

> Does anyone has a clue, what is going wrong? Since my ncbi.ini - file 
> points to the directory, where blosum62 is found, I can not understand 
> this error-message.

It really looks like it can't find BLOSUM62, which indicates that the 
ncbi.ini file is not being read, or has the wrong syntax.

Those "/" forward slashes look potentially problematic on a Windows 
platform - perhaps try using "\" backslashes. ie.

	[NCBI]
	Data="D:\BLAST\BLAST-2.2.13\data"
(Continue reading)

Chris Fields | 2 Mar 13:38 2006
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Re: Bio::Tools::Run::* extending

Look at bioperl-run:

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

You can look over these modules for ideas, hints, etc.

Chris

On Mar 2, 2006, at 2:53 AM, Rutger Vos wrote:

> Hi all,
>
> I'd like to write some more Bio::Tools::Run::* wrappers, so I'm
> wondering what the canonical approach is. Which libraries *should* I
> look at (as examples of the bioperl received wisdom and coding
> standards) and which ones *shouldn't* I look at? I'm thinking that  
> paup,
> mrbayes and modeltest need wrappers.
>
> Thanks!
>
> Rutger
>
> -- 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> Rutger Vos, PhD. candidate
> Department of Biological Sciences
> Simon Fraser University
> 8888 University Drive
> Burnaby, BC, V5A1S6
(Continue reading)


Gmane