[Bioperl-l] need help urgently

[Chris Fields]

Neeti,

Sorry, it's a package deal (and Bio::DB::EUtilities relies on several  
other modules).  I am planning on spinning it out at some point into  
it's own package, but for now the easiest way to install is via 1.6  
off CPAN or downloading the nightly build:

http://www.bioperl.org/DIST/nightly_builds/

chris

On Sep 4, 2009, at 7:40 AM, Neeti Somaiya wrote:

> Hi,
>
> Thanks for your reply. I saw this before and wanted to try this, but I
> am unable to install this module of EUtilities. When I search on CPAN,
> it gives me the entire bioperl package in the download option of this
> module. Can I not get a tar.gz file of this module alone, which I can
> gzip, untar and then run the make and all to install it? I dont want
> to install entire bioperl again as I am using an older version. Any
> suggestions?
>
> -Neeti
> Even my blood says, B positive
>
>
>
> On Fri, Sep 4, 2009 at 6:00 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>> Neeti,
>>
>> Something like this?
>>
>> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#esummary_-.3E_efetch
>>
>> chris
>>
>> On Sep 4, 2009, at 7:21 AM, Neeti Somaiya wrote:
>>
>>> Thanks. Its an interesting tool.
>>>
>>> But I want to do this programatically.
>>>
>>> I have gene ids to start with. Cant find a method to directly get
>>> sequence with gene id as input. So using the method of getting
>>> sequence with accession as input, for which I need to know  
>>> accessions
>>> for my gene ids first. Is this a right approach? Please guide me. My
>>> main aim is to get the nucleotide sequence of a gene from ids entrez
>>> gene id/gene name. PLease guide me. I am confused.
>>>
>>> -Neeti
>>> Even my blood says, B positive
>>>
>>>
>>>
>>> On Fri, Sep 4, 2009 at 5:35 PM, Emanuele Osimo<e.osimo at gmail.com>  
>>> wrote:
>>>>
>>>> Try this:
>>>> http://david.abcc.ncifcrf.gov/conversion.jsp
>>>>
>>>> Emanuele
>>>>
>>>>
>>>> On Fri, Sep 4, 2009 at 12:13, Neeti Somaiya  
>>>> <neetisomaiya at gmail.com>
>>>> wrote:
>>>>>
>>>>> Thanks for the replies.
>>>>>
>>>>> So the get seq by accession/GI worked for me. Now can anyone  
>>>>> tell me
>>>>> the easiest way to get the GI /Accession of a gene from the gene
>>>>> id/gene name?
>>>>>
>>>>> -Neeti
>>>>> Even my blood says, B positive
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Sep 4, 2009 at 2:47 PM, Neeti Somaiya<neetisomaiya at gmail.com 
>>>>> >
>>>>> wrote:
>>>>>>
>>>>>> Thanks for the link.
>>>>>> So I need only the following lines of code to get the sequence?
>>>>>>
>>>>>> use Bio::DB::GenBank;
>>>>>> $db_obj = Bio::DB::GenBank->new;
>>>>>> $seq_obj = $db_obj->get_Seq_by_id(2);
>>>>>>
>>>>>> How do I print the sequence?
>>>>>> $seq_obj->seq ??
>>>>>>
>>>>>> -Neeti
>>>>>> Even my blood says, B positive
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 4, 2009 at 1:31 PM, K. Shameer<shameer at ncbs.res.in>  
>>>>>> wrote:
>>>>>>>
>>>>>>> Retrieving a sequence from a database : BioPerl HOWTO
>>>>>>> http://bit.ly/RWIot
>>>>>>>
>>>>>>> Trust this helps,
>>>>>>> Khader Shameer
>>>>>>> NCBS - TIFR
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have an input list of gene names (can get gene ids from a  
>>>>>>>> local db
>>>>>>>> if required).
>>>>>>>> I need to fetch sequences of these genes. Can someone please  
>>>>>>>> guide me
>>>>>>>> as to how this can be done using perl/bioperl?
>>>>>>>>
>>>>>>>> Any help will be deeply appreciated.
>>>>>>>>
>>>>>>>> Thanks.
>>>>>>>>
>>>>>>>> -Neeti
>>>>>>>> Even my blood says, B positive
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
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