[Bioperl-l] Bioperl installation doubt

[¶•●๋•இரவிяανι●๋••¶]

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
>>>>
>>>
>>>
>>
>