[Bioperl-l] need help urgently

Sat Sep 5 07:37:58 UTC 2009

Ok,
this is what I would do.
Download the database of gene names and sequences in fasta.
Then loop throught it with bioperl.
Regex the gene names, which you store into a hash, against the
seq->display_names() should match it up with gene ids
seq->seq() should print out the sequence
in bioperl.
Print out the ones that match.
Good luck.
- Show quoted text -

On Thu, Sep 3, 2009 at 11:49 PM, Neeti Somaiya<neetisomaiya at gmail.com> wrote:
> 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
>


--

On Fri, Sep 4, 2009 at 9:52 PM, Neeti Somaiya<neetisomaiya at gmail.com> wrote:
> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> _______________________________________________
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-- 
Eugene Bolotin
Ph.D. candidate
Genetics Genomics and Bioinformatics
University of California Riverside
ybolo001 at student.ucr.edu
Dr. Frances Sladek Lab