[Bioperl-l] Bioperl installation doubt

Dave Messina David.Messina at sbc.su.se
Mon Mar 28 08:45:34 EDT 2011


Again, please "Reply All" so that your messages go to the mailing list.

Ravi, PLEASE read the documentation on the website first and try to figure
out how to solve your problem on your own. BioPerl is a complex system and
requires some effort to learn how to use. I and everyone on this list
volunteers our time answering questions, and we are happy to do so, but you
have to meet us halfway.


Dave




2011/3/28 ¶•●๋•இரவிяανι●๋••¶ <ravimbt at gmail.com>

> Hi Dave,
>
> Thanks for the information. I have also signed up to join the forum.
>
> I could not retrieve the sequence from other databases other than Genbank.
> Could you please do the changes on the below programme to make it working so
> that I can try in my system.
> --------------------
> use Bio::Perl;
>
> $seq_object = get_sequence('genbank',"ECORHO");
>
> write_sequence(">ael.fasta",'fasta',$seq_object);
> ------------------
>
> Thanks once again.
>
> With regards,
> Ravi.
>
>
> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
>
>> Thank you very much. It is working. I got the program code from the
>>> following link.
>>>
>>> http://www.bioperl.org/Core/Latest/bptutorial.html
>>
>>
>> Aha, okay. You got there from Google, I guess? That is *way* out of date.
>>
>> To the other core devs, in order to prevent this confusion in the future,
>> I'd like to delete the Core/ directory from our website since it's been
>> superseded at this point by other docs and is not current. I intend to put
>> up a ticket at Redmine, but I will wait a bit before doing so to allow time
>> for people to see this and comment — please do speak up if there's good
>> reason to keep it.
>>
>>
>> Could you please give me the link to join this forum to see other
>>> discussions, which would be more helpful to me?
>>>
>>
>> Sure, you can sign up for the mailing list here:
>>
>>  <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> And the archives are also searchable:
>>
>>     http://news.gmane.org/gmane.comp.lang.perl.bio.general
>>
>>
>> Please let me know if you have any suggestion for me to keep learning the
>>> bioperl.
>>
>>
>> I would also suggest reading the (current) tutorial and HOWTOs at
>> www.bioperl.org . Lots of good links on the main page there, particularly
>> under the Documentation heading.
>>
>>
>> Dave
>>
>>
>>
>>
>>
>>> 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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