[Bioperl-l] need help urgently

[Neeti Somaiya]

Ok, so I reinstalled bioperl and was able to run the EUtilities code
for my gene id.
But I am facing two issues :-

1) When I give multiple gene ids, it still returns data of only the
first gene id

2) The script returns the entire entry, and I am not able to figure
out how to just fetch the sequence, and if possible, in FASTA format.
I could not figure it out from the documentation.

Thanks.

-Neeti
Even my blood says, B positive



On Fri, Sep 4, 2009 at 6:19 PM, Chris Fields<cjfields at illinois.edu> wrote:
> 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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