[Bioperl-l] how to download PDB files using Bioperl script

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Nov 2 22:11:36 EDT 2010


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



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.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Regards,
Chirag Matkar
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================




More information about the Bioperl-l mailing list