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Will Bryant | 1 Jun 10:06
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Extract genomic data from GenBank

I'm trying to retrieve the complete GenBank format sequence file for a 
specified bacterium using get_Seq_by_gi, but I keep getting 'gi does not 
exist' errors, even when trying the example gi '405830'.  The script was 
running fine September last year, but when I came back to it this week 
it wasn't working.  Am I missing something obvious?

In case it's important, I'm using ActivePerl 5.10.0, bioperl 1.5.2_100

Code:

#!/usr/bin/perl -w

use strict;
use Bio::Perl;
use Bio::DB::GenBank;

my $gb = new Bio::DB::GenBank(-db => 'genome', -format => 'genbank');

my $straincomp = $gb->get_Seq_by_gi('405830');

my $seqout = 0;

#my $set_output_file = '$seqout = Bio::SeqIO->new( -format => 
\'genbank\', -file => 
\'>c:\\phd\\modelling\\working\\gi'.$ARGV[0].'_data.gb\');';

#print $set_output_file;
eval ($set_output_file);

$seqout -> write_seq($straincomp);
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Dave Messina | 1 Jun 11:04
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Re: Extract genomic data from GenBank

Hey Will,
I think there have been API changes in GenBank's remote query interface that
have occurred after 1.5.2_100 of BioPerl was written. Try upgrading to
BioPerl 1.6 and see if that works for you.

(Note that I've only glanced at your code -- I'm assuming that's not the
problem since it worked fine for you before.)

Dave
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Kristina Fontanez | 1 Jun 14:41
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Re: problem with bioperl install

Hey everyone-

Thanks for all the advice. I reinstalled Xcode tools, installed Fink  
and downloaded bioperl successfully. It's now working smoothly.

Thanks again,
Kristina
---------------------------------------------------------------
Kristina Fontanez
PhD candidate
Department of Organismic and Evolutionary Biology
Cavanaugh lab
Harvard University
16 Divinity Ave.
Cambridge, MA 02138

tel: 617-495-1138
fax: 617-496-6933
email: fontanez <at> fas.harvard.edu

On May 29, 2009, at 10:40 PM, Chris Fields wrote:

Kristina,

You aren't running as superuser:

 > term dump: > > dhcp-0019353043-25-35:BioPerl-1.6.0 kristinafontanez 
$ cpan

You'll need to run cpan using 'sudo cpan' if installing modules
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Mark A. Jensen | 1 Jun 16:55
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a HOWTO for Tiling

Hi All 
Please peruse http://www.bioperl.org/wiki/HOWTO:Tiling for an exhibition of B::S::Tiling, use
cases, code snippets, design, implementation and algorithm discussions. We're just about ready to port
over to core from bioperl-dev; please shout out if this is not a good idea. 
cheers and thanks for all input--
Mark
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Chris Fields | 1 Jun 17:21
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Re: problem with bioperl install

A autogenerated passthrough Makefile.PL is generated with the  
distribution:

http://cpansearch.perl.org/src/CJFIELDS/BioPerl-1.6.0/Makefile.PL

We may remove that in future releases, but it should work regardless  
(i.e. call Module::Build and Build.PL).  I'm pretty convinced that the  
issue was permissions-based at heart.  Note Kristina ran 'cpan'  
instead of 'sudo cpan' to invoke the shell, so the shell is using  
current user config instead of su for installation.  You need to use  
'sudo' to install anything /Library/Perl on Mac (unless you are  
already 'root', but on recent OS X version logging in as 'root' is  
turned off).

I just noticed nothing is mentioned along these lines in the  
installation docs, so we'll need to update those.

chris

On May 29, 2009, at 4:08 PM, Mark A. Jensen wrote:

> Hi Kristina,
>
> [Don't forget to reply-all, so the list stays in the loop. Many many  
> more helpers
> there.]
>
> Apparently cpan can't make the Makefile, but can download and expand  
> the
> library directories, in your .cpan directory (see edited highlights
(Continue reading)

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Chris Fields | 1 Jun 18:14
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Re: a HOWTO for Tiling

I think, as long is it doesn't significantly impact SearchIO  
performance wise (from reading the HOWTO I can't see how it will), I  
say commit away. In fact, I consider this a bug fix that should be in  
the next 1.6 point release. We should add deprecation warnings where  
needed for 1.7...

chris

On Jun 1, 2009, at 9:55 AM, Mark A. Jensen wrote:

> Hi All
> Please peruse http://www.bioperl.org/wiki/HOWTO:Tiling for an  
> exhibition of B::S::Tiling, use cases, code snippets, design,  
> implementation and algorithm discussions. We're just about ready to  
> port over to core from bioperl-dev; please shout out if this is not  
> a good idea.
> cheers and thanks for all input--
> Mark
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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Dan Bolser | 1 Jun 18:27
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Re: problem with bioperl install

2009/6/1 Chris Fields <cjfields <at> illinois.edu>:

...
> for installation.  You need to use 'sudo' to install anything /Library/Perl
> on Mac (unless you are already 'root', but on recent OS X version logging in
...

local::lib is supposed to take care of this. Is this broken on Mac?
Building stuff as root is generally considered to be bad.

> I just noticed nothing is mentioned along these lines in the installation
> docs, so we'll need to update those.

I tried to write down a clear 'recipe' for getting things installed
(this was actually on the GMod wiki). I really think the install docs
could be improved. Sometimes less verbose is better.

Dan

> chris
>
> On May 29, 2009, at 4:08 PM, Mark A. Jensen wrote:
>
>> Hi Kristina,
>>
>> [Don't forget to reply-all, so the list stays in the loop. Many many more
>> helpers
>> there.]
>>
>> Apparently cpan can't make the Makefile, but can download and expand the
(Continue reading)

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Chris Fields | 1 Jun 19:15
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Re: problem with bioperl install


On Jun 1, 2009, at 11:27 AM, Dan Bolser wrote:

> 2009/6/1 Chris Fields <cjfields <at> illinois.edu>:
>
> ...
>> for installation.  You need to use 'sudo' to install anything / 
>> Library/Perl
>> on Mac (unless you are already 'root', but on recent OS X version  
>> logging in
> ...
>
> local::lib is supposed to take care of this. Is this broken on Mac?
> Building stuff as root is generally considered to be bad.

You can install to a local lib, yes, but cpan needs to be manually  
configured to do this; I don't think it is automatically configured to  
do so in OS X, eg. it defaults to /Library/Perl.

Frankly, I sidestep the whole issue with my own custom perl  
installation, but that's me.

>> I just noticed nothing is mentioned along these lines in the  
>> installation
>> docs, so we'll need to update those.
>
> I tried to write down a clear 'recipe' for getting things installed
> (this was actually on the GMod wiki). I really think the install docs
> could be improved. Sometimes less verbose is better.
>
(Continue reading)

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Mark A. Jensen | 1 Jun 21:03
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Re: a HOWTO for Tiling

Thanks, Chris--

Bio::Search::Tiling is now ported to core; the snapshot of the ported version is 
in bioperl-dev/tags/tiling-port-to-core-060109.
Bunch o' tests performed by t/SearchIO/Tiling.t; bunch more if one sets 
BIOPERL_TILING_EXHAUSTIVE_TESTS .

Cry 'Havoc!' and let slip the dogs of war...

MAJ

----- Original Message ----- 
From: "Chris Fields" <cjfields <at> illinois.edu>
To: "Mark A. Jensen" <maj <at> fortinbras.us>
Cc: "Sendu Bala" <bix <at> sendu.me.uk>; "Dave Messina" <dave <at> davemessina.com>; 
"BioPerl List" <bioperl-l <at> lists.open-bio.org>
Sent: Monday, June 01, 2009 12:14 PM
Subject: Re: [Bioperl-l] a HOWTO for Tiling

>I think, as long is it doesn't significantly impact SearchIO  performance wise 
>(from reading the HOWTO I can't see how it will), I  say commit away. In fact, 
>I consider this a bug fix that should be in  the next 1.6 point release. We 
>should add deprecation warnings where  needed for 1.7...
>
> chris
>
> On Jun 1, 2009, at 9:55 AM, Mark A. Jensen wrote:
>
>> Hi All
>> Please peruse http://www.bioperl.org/wiki/HOWTO:Tiling for an  exhibition of
(Continue reading)

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Koen van der Drift | 2 Jun 00:22
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Re: problem with bioperl install


On Jun 1, 2009, at 1:15 PM, Chris Fields wrote:

> My thought is to strip down the INSTALL doc that comes with BioPerl  
> down to the essentials and point to the wiki for the more detailed  
> ones (including problems encountered).  It's too hard to maintain  
> both and backport the wiki into plain text.

Good idea, please then also update the file PLATFORMS. It has a link  
to a very outdated website for the installation of bioperl on OS X.  
And maybe a line + link to the bioperl wiki can be added that  
recommends the use of fink as an alternative to cpan?

cheers,

- Koen.
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Gmane