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Gabrielle Doan | 1 Jul 2008 10:29
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Problems when trying to persist a sequence in my BioSQL database using BioPerl

Hi Hilmar and Sendu,

thanks a lot for your help! After installing the latest version of
Scalar::Util I didn't get the error anymore. Unfortunately, I'm facing
an other problem. I tried to insert the Genbank file of the human
Chromosome 1 - downloaded from the NCBI
(ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz) -
into my BioSQL database with a perl script (load_seqdatabase.pl from the 
BioPerl db package), but after about one hour I received the message
'Out of memory'. After the abort I have only 13 entries in my database.
I can't image that four GB RAM are not sufficient. Does anybody have the
same problem? I am greateful for any hint!

Cheers,
Gabrielle
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Captainrave | 1 Jul 2008 10:19
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re ading in cds, outputting products


How would I use bioperl to read in CDS positions (maybe in csv format in a
list), find the releated products and/or genes for each and output these
into a new csv file or similar file?
--

-- 
View this message in context: http://www.nabble.com/reading-in-cds%2C-outputting-products-tp18211537p18211537.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
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Pallavi Sarmah | 2 Jul 2008 09:36
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not being able to install Bio-ext-1.4


Hi

I am having problem installing Bio::Ext-1.4.  I have forced installed BioPerl1.4 and now trying to install
Bio::Ext but getting the following errors in Ubuntu. This is not the full list of errors but I am not being
able to get all. Can anyone please help me with this. I have been trying the mailing list for quite sometime now.

Align.c:5835: error: array subscript is not an integer
Align.c:5835: error: array subscript is not an integer
Align.c:5835: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: array subscript is not an integer
Align.c:5836: error: too many arguments to function ‘Perl_sv_2pv_flags’
Align.c:5838: error: ‘OP’ has no member named ‘op_private’
Align.c:5838: error: ‘OP’ has no member named ‘op_targ’
Align.c:5842: error: invalid operands to binary +
Align.c:5842: error: ‘IV’ undeclared (first use in this function)
Align.c:5842: error: expected ‘)’ before ‘RETVAL’
Align.c:5842: error: too many arguments to function ‘Perl_sv_setiv’
Align.c:5842: error: ‘SV’ has no member named ‘sv_flags’
Align.c:5844: error: expected ‘;’ before ‘tmpXSoff’
Align.c:5844: error: invalid operands to binary +
Align.c:5844: error: ‘tmpXSoff’ undeclared (first use in this function)
Align.c: In function ‘XS_Bio__Ext__Align__FileSource_filename’:
Align.c:5851: error: function ‘ax’ is initialized like a variable
Align.c:5851: error: invalid lvalue in increment
Align.c:5851: error: function ‘items’ is initialized like a variable
Align.c:5852: warning: comparison between pointer and integer
Align.c:5855: error: array subscript is not an integer
(Continue reading)

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Nathan Haseley (RIT Student | 2 Jul 2008 16:34
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Clustalw module

Hello,
   I am working with the Bioperl module Bio::Tools::Run::Alignment::Clustalw.  I try to include the package
in my script as follows:

#!/usr/bin/perl
use Bio::Seq;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;
use Bio::DB::GenBank;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::Root::Exception;
use Error qw(:try);

but I keep getting the following error message:
Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in  <at> INC ( <at> INC contains: /etc/perl
/usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5
/usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6.
BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6.

The Clustalw program is configured correctly to work in my directory.  Am I missing something obvious or is
there something wrong with my BioPerl configuration?  Any advice on how to fix this?  Thank you for your time.

Nathan
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Jason Stajich | 2 Jul 2008 17:02
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Re: Clustalw module

did you install bioperl-run package as well as bioperl core?
-jason
On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote:

> Hello,
>    I am working with the Bioperl module  
> Bio::Tools::Run::Alignment::Clustalw.  I try to include the package  
> in my script as follows:
>
> #!/usr/bin/perl
> use Bio::Seq;
> use Bio::SearchIO;
> use Bio::Tools::Run::StandAloneBlast;
> use Bio::DB::GenBank;
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::Root::Exception;
> use Error qw(:try);
>
> but I keep getting the following error message:
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in  <at> INC ( <at> INC  
> contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ 
> 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ 
> perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6.
> BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6.
>
> The Clustalw program is configured correctly to work in my  
> directory.  Am I missing something obvious or is there something  
> wrong with my BioPerl configuration?  Any advice on how to fix  
> this?  Thank you for your time.
>
(Continue reading)

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Kevin Brown | 2 Jul 2008 17:10
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Re: not being able to install Bio-ext-1.4

Bioperl 1.4 is more than 5 years old.  Try following the install
instructions on the bioperl website for a more up2date version (v1.5.2):

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

Or

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

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org 
> [mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of 
> Pallavi Sarmah
> Sent: Wednesday, July 02, 2008 12:36 AM
> To: ymc <at> paxil.stanford.edu; birney <at> sanger.ac.uk; bioperl-l <at> bioperl.org
> Subject: [Bioperl-l] not being able to install Bio-ext-1.4
> 
> 
> Hi
> 
> I am having problem installing Bio::Ext-1.4.  I have forced 
> installed BioPerl1.4 and now trying to install Bio::Ext but 
> getting the following errors in Ubuntu. This is not the full 
> list of errors but I am not being able to get all. Can anyone 
> please help me with this. I have been trying the mailing list 
> for quite sometime now.
> 
> Align.c:5835: error: array subscript is not an integer
> Align.c:5835: error: array subscript is not an integer
> Align.c:5835: error: array subscript is not an integer
(Continue reading)

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Jason Stajich | 2 Jul 2008 17:25
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Re: Clustalw module

re: StandAloneBlast and RemoteBlast - due to their perceived  
widespread use was not moved from the core package to run so they  
come in with the basic Core modules install package.
Given the error message I would again say that the bioperl-run was  
not installed.

If you do perldoc ModuleName it will tell you if the module can be  
found.

locate Clustalw.pm can also help you locate if it is installed but  
just not in PERL5LIB path.

-jason

On Jul 2, 2008, at 11:04 AM, Nathan Haseley (RIT Student) wrote:

> I am running my script on a remote server, so I didn't do the  
> installation.  I would assume so, however, since StandAloneBlast  
> works fine.
> Nathan
>
>
> -----Original Message-----
> From: Jason Stajich on behalf of Jason Stajich
> Sent: Wed 7/2/2008 11:02 AM
> To: Nathan Haseley (RIT Student)
> Cc: bioperl-l <at> lists.open-bio.org
> Subject: Re: [Bioperl-l] Clustalw module
>
> did you install bioperl-run package as well as bioperl core?
(Continue reading)

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RICHARD GREEN | 2 Jul 2008 20:10

finding sequence 2000 bp upstream in bioperl?

Howdy Bioperlers,

Quick question, I have scripts that pull out a sequence from genbank, but I am looking for a command that
would extract 2000 base pairs upstream of the sequence. Is there a way to extract just the Gene promoter
region from genbank? Any advice that folks can give me a is muchly appreciated.

Thanks again

-Rich Green
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Kevin Brown | 2 Jul 2008 21:36
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Re: finding sequence 2000 bp upstream in bioperl?

Get the start point for a Sequence Feature and request a subseq of the
main object that starts 2000 above that.

my $gb  = new Bio::DB::GenBank;
$entry = $gb->get_Seq_by_id($id);
foreach my $f ($entry->all_SeqFeatures())
{
	if ($f->primary_tag eq 'CDS')
	{
		my $seq = $entry->subseq($f->start - 2000,$f->start -
1);
		$out->write_seq($seq);
	}
}

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org 
> [mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of 
> RICHARD GREEN
> Sent: Wednesday, July 02, 2008 11:10 AM
> To: bioperl-l <at> lists.open-bio.org
> Subject: [Bioperl-l] finding sequence 2000 bp upstream in bioperl?
> 
> Howdy Bioperlers,
> 
> Quick question, I have scripts that pull out a sequence from 
> genbank, but I am looking for a command that would extract 
> 2000 base pairs upstream of the sequence. Is there a way to 
> extract just the Gene promoter region from genbank? Any 
> advice that folks can give me a is muchly appreciated.
(Continue reading)

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snoze pa | 2 Jul 2008 21:56
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Install help errors

Dear Users,
 I am trying to install bioperl in fedora machine. I am using
precompiled rpm from fedora repo. it is installed. Next I download the
biosql and put in a dir /usr/local/biosql
create a database bioseqdb and load the scema.

However the bioperl-db is not working.. it is giving lots of error. I
used CPAN and also the perl Build.PL. following are the results

Please help me.
thank you.

Test Summary Report
-------------------
t/04swiss     (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 52 tests but ran 5.
t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 48 tests but ran 3.
t/06comment   (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 11 tests but ran 2.
t/07dblink    (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 18 tests but ran 2.
t/08genbank   (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 18 tests but ran 2.
t/09fuzzy2    (Wstat: 65280 Tests: 2 Failed: 0)
(Continue reading)

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Gmane