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chirag matkar | 1 Nov 2010 07:58
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Re: how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;

Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data

On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu <at> gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
(Continue reading)

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Smithies, Russell | 3 Nov 2010 03:11
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Re: how to download PDB files using Bioperl script

Seems a bit like overkill, what's wrong with wget?

wget -i <list_of_urls.txt>

--Russell

-----Original Message-----
From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-bounces <at> lists.open-bio.org] On
Behalf Of chirag matkar
Sent: Monday, 1 November 2010 7:59 p.m.
To: bioperl-l <at> lists.open-bio.org
Subject: Re: [Bioperl-l] how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;

Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data
(Continue reading)

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Miguel Pignatelli | 3 Nov 2010 10:42
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Another Taxonomy modules to CPAN

Hi all,

I have written a couple of modules that overlap certain functionality 
with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
certain constraints in the environment I had to run it (GRID) made 
impossible to use a bioperl based solution.

The main features of these modules are:

+ No dependencies of non-standard Perl modules
+ NCBI and RDP based taxonomies supported
+ Very fast and low memory footprint -- orders of magnitude faster than 
Bioperl modules (for the tasks they are designed for --).

Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in 
completeness or integration with other tools (e.g. rest of bioperl suit) 
but they are handy for mapping very large datasets (for example blast 
results) with the NCBI or RDP Taxonomy.

The modules are:

Taxonomy::Base -- Finds ancestors, ranks, converts between
                   names, ranks and IDs, etc...

Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file

Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
                   (nodes.dmp and names.dmp)
                   (Similar to Bio::DB::Taxonomy::flatfile)
(Continue reading)

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gabriel teku | 3 Nov 2010 12:53
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Bio::DB::EUtilities esearch PhraseNotFound error

I can't get my esearch to work. It's as follows:

my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
                                                  -email      => '
myemail <at> gmail.com',
                                                  -term       =>
'$genename[SYMB] AND homo_sapiens[ORGN]',
                                                  -db         => 'geo',
                                                  -usehistory => 'y'
                                              );

When I run this using a gene symbol, it works fine.
But then when I run it as it is with a gene's symbol changed to
$genename(stores the gene's symbol/name), it fails.
How can this be fixed?

Thanks
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Miguel Pignatelli | 3 Nov 2010 14:51
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SFF format support

Hi all,

I have seen in the Nextgen section of the bioperl wiki 
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in 
the wish list. I have some code written for parsing SFF files that I can 
refactor and contribute with it.

Does anyone already took this?

Best regards,

M;
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Peter | 3 Nov 2010 15:28
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Re: SFF format support

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli <at> uv.es>:
> Hi all,
>
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
>
> Does anyone already took this?
>
> Best regards,
>
> M;

Hi,

This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.

Peter
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Scott Cain | 3 Nov 2010 15:59
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Re: Bio::DB::EUtilities esearch PhraseNotFound error

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:

  $genename[SYMB]

looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.

Scott

On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku <at> gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
>
> my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
>                                                  -email      => '
> myemail <at> gmail.com',
>                                                  -term       =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
>                                                  -db         => 'geo',
(Continue reading)

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Chet Seligman | 3 Nov 2010 17:07
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BioPerl installation was incomplete

My perl is ActiveState 5.10.1

I installed with PPM using the following repositories:

BioPerl-Regular Releases

BioPerl-Release Candidates

Kobes

Bribes

Trouchelle

I got the following warnings:

Can't find any package that provides DB_File:: for Bundle-BioPerl-Core

WARNING: Can't find any package that provides IPC::Run for GraphViz

WARNING: Can't find any package that provides Apache:: for SOAP-Lite

I do have DB_File installed but do not have:

IPC::Run or,

Apache:: for SOAP-Lite

I did try to install SOAP-Lite according to the instructions in the Wiki but
no luck.
(Continue reading)

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Chris Fields | 3 Nov 2010 18:18
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Re: SFF format support

Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork
the code, hack away, and submit pull requests), but we also accept patches.  

I suggest, though, for long-term maintenance you could be added as a collaborator.  

chris

On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have seen in the Nextgen section of the bioperl wiki
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some
code written for parsing SFF files that I can refactor and contribute with it.
> 
> Does anyone already took this?
> 
> Best regards,
> 
> M;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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hanbobio | 2 Nov 2010 06:29
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bioperl modules

Hi, all.
 I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were
some mistake, the following was the message the linux system feelback:

liaoy <at> linux:~/nd-hn> perl nd-hn.pl

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in  <at> INC ( <at> INC contains:
/usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7
/usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.

BEGIN failed--compilation aborted at nd-hn.pl line 26.
 The detail of this script in two ways: the attached file and the following script.
Would you be kindly to test my script and give me some modification or suggestion?
 I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from
remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment
outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment)
encountered some problem? What the problem is? How can I correct it?
Thank you very much for your advice.

Best regards
Yusheng Liao 2010-11-02

# retrive sequence from Genbank
use strict;
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
my $query = Bio::DB::Query::GenBank->new
(Continue reading)

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Gmane