[Bioperl-l] Bioperl installation doubt

Chris Fields cjfields at illinois.edu
Wed Mar 30 09:58:00 EDT 2011


Ravi,

You can sign up for the email list here:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

Once you are signed up, you should be able to post questions.

chris

On Mar 28, 2011, at 4:56 AM, ¶•●๋•இரவிяανι●๋••¶ wrote:

> Hi Dave,
> 
> Thank you very much. It is working. I got the program code from the
> following link.
> 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> 
> I spent so much time on browsing, downloading and installing programs and
> packages. But, it seems like the code error is the reason it dint work.
> Thanks Dave.
> 
> Could you please give me the link to join this forum to see other
> discussions, which would be more helpful to me? Please let me know if you
> have any suggestion for me to keep learning the bioperl.
> 
> With regards,
> Ravi.
> 
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> 
>> Hi Ravi,
>> 
>> Please make sure to "Reply All" so that everyone on the mailing list can
>> follow (and add to) the discussion.
>> 
>> If you read the first line of the exception, you'll see it states what the
>> error is:
>> "WebDBSeqI Error — check query sequences!"
>> 
>> You'd have no way of knowing this, but that ID and database combination is
>> not functioning anymore, so that's why in this case you're getting an error.
>> Please try using the example in the tutorial here:
>> 
>> 
>> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
>> 
>> which has been updated to a different ID which should work.
>> 
>> Sorry for the confusion! So that we can prevent other people from having
>> the same issue, could you tell me where you got that example code?
>> 
>> Dave
>> 
>> 
>> 
>> 
>> 
>> 
>> 2011/3/28 ¶•●๋•இரவிяανι●๋••¶ <ravimbt at gmail.com>
>> 
>>> Hi Dave,
>>> 
>>> Thanks a lot for your reply. It is really helpful. Please find the
>>> screenshot after making the change you pointed out. But I am getting
>>> "Exception: Bio::Root::Exception" error. I think I have to set the
>>> environment variables but I am not sure how to do that. Could you please
>>> guide me on this too.
>>> 
>>> I can go to the "Environment Variable" Window in my pc. But I dont know
>>> what to enter once I click "New" on that window.
>>> 
>>> Thanks in advance.
>>> 
>>> With regards,
>>> Ravi.
>>> 
>>> 
>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
>>> 
>>>> Hi Ravi,
>>>> 
>>>> The get_sequence and write_sequence methods are in the Bio::Perl module,
>>>> not Bio::Seq. So your first line
>>>> 
>>>> use Bio::Seq;
>>>> 
>>>> should be replaced with
>>>> 
>>>> use Bio::Perl;
>>>> 
>>>> 
>>>> More examples in the BioPerl Tutorial here:
>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
>>>> 
>>>> 
>>>> Dve
>>>> 
>>>> 
>>>> 
>>>> 2011/3/24 ¶•●๋•இரவிяανι●๋••¶ <ravimbt at gmail.com>
>>>> 
>>>>> Hi,
>>>>> 
>>>>> Could you please help me installing bioperl-db, bioperl-run & other
>>>>> packages
>>>>> using ppm on windows 7? Please find the attachment for the error message
>>>>> I
>>>>> get. I would really appreciate if you help me fix this issue.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> With regards,
>>>>> Ravi.
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> 
>>> 
>> 
> 
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