[Bioperl-l] Zombie processes with GenBank get_Seq_by_acc()

[Roy Chaudhuri]

That's not really true. Turning on strict just makes it a compile time 
error if you don't declare the scope of a variable. "my" and "our" will 
still work without turning on strict, but they are not mandatory. Of 
course, you should always use strict, it's there to help you.

@lines[$i] is valid syntax, although you will get the message "Scalar 
value @lines[$i] better written as $lines[$i]" if warnings are switched 
on (again, this should always be the case).

Roy.

On 12/05/2011 16:20, Kevin Brown wrote:
> Utilizing keywords like "my", "our", etc... is only useful in perl if
> you also "use strict;" in your script. This forces perl to deal with
> variable scope and should cause those threads to die when the parent
> object goes out of scope. Instead they aren't dying because their parent
> object never gets destroyed.
>
> In fact, going through your code showed that you had a large number of
> errors such as @lines[$i] is NOT how you get something out of an array.
> $lines[$i] is.
>
> http://pastebin.com/vx9Y0GW7
>
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of O'car Campos
>> Sent: Thursday, May 12, 2011 6:57 AM
>> To: Dave Messina
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Zombie processes with GenBank
> get_Seq_by_acc()
>>
>> Dave:
>>
>>         Thanks for checking the code, I tried with what you said,
> adding
>> a
>> "my" to line 18 but I still get the zombies. I was exaggerating with
>> the
>> 8000 genbank codes, also I didn't know about those other tools I will
>> check
>> them, thanks for the tip. So I'm still in a zombieland.
>>
>> Cheers.
>>
>> O'car
>>
>>
>> On 12 May 2011 03:22, Dave Messina<David.Messina at sbc.su.se>  wrote:
>>
>>> Thanks for posting the code, O'car.
>>>
>>> I haven't tried running it, but one thing that occurs to me is that
>> on line
>>> 18 when you create your Bio::DB::Genbank object, there's no 'my', so
>> those
>>> objects may be hanging around longer than you expect. The zombies
> may
>> be
>>> those objects' forked processes for connecting to Genbank. Similar
> to
>> what
>>> Kevin said earlier.
>>>
>>> But that's all speculation.
>>>
>>> The other thing I'll say as a general comment is that fetching
>> thousands of
>>> records from Genbank this way (or really fetching any more than 100)
>> is
>>> inefficient and probably slow also.
>>>
>>> Instead you might try using Genbank's own fetching tools,
> EUtilities,
>>> either directly or via the two BioPerl interfaces to them
>>> (Bio::DB::EUtilities and Bio::DB::SoapEUtilities).
>>>
>>>
>>> Dave
>>>
>>>
>>>
>>>
>>> On Thu, May 12, 2011 at 00:16, O'car Johann Campos
>> <ocarnorsk138 at gmail.com
>>>> wrote:
>>>
>>>> Kevin Brown<Kevin.M.Brown<at>  asu.edu>  writes:
>>>>
>>>>>
>>>>> Seeing your code might help. They could just be forked children
>> waiting
>>>>> for the script to exit before they go away or something else
>> forked them
>>>>> and failed to clean up before quitting.
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces<at>  lists.open-bio.org
> [mailto:bioperl-
>> l-
>>>>>> bounces<at>  lists.open-bio.org] On Behalf Of Belaid MOA
>>>>>> Sent: Tuesday, May 10, 2011 1:41 PM
>>>>>> To: bioperl-l<at>  lists.open-bio.org
>>>>>> Subject: [Bioperl-l] Zombie processes with GenBank
>> get_Seq_by_acc()
>>>>>>
>>>>>>
>>>>>> Dear All,
>>>>>>    I installed the latest version of BioPerl and I ran a very
>> simple
>>>>>> code: it goes through each line (an ACC) in a file and uses
>> GenBank to
>>>>>> get the sequence
>>>>>> via get_Seq_by_acc(). A look at ps shows that there were a lot
>> of
>>>>>> zombie processes (with<defunct>  attribute) created. The list
>> grows
>>>>>> with the time.
>>>>>> This means that Bio:DB:GenBank is forking and not cleaning the
>>>>>> children. Is there any way to overcome the issue? Moreover, is
>> there
>>>>>> any way
>>>>>> to specify the number of forked processes?
>>>>>>
>>>>>> With best regards,
>>>>>> -Belaid.
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l<at>  lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>> Kevin, Belaid, All:
>>>>
>>>>         Recently I've been working with genbank too and ran a code
> to
>> get
>>>> Genbank info from accession numbers, I also noticed the weird
>> behavior and
>>>> the
>>>> zombie processes that are in the background, altough the code works
>> and I
>>>> get
>>>> the info I need there are a lot of zombie processes in the
>> background and
>>>> for
>>>> example running this task with 8000 accession numbers would be a
>> pain
>>>> where you
>>>> all know. I'm not a bioperl expert and I may be missing some piece
>> of code
>>>> to
>>>> quit the forked children as may be happening to belaid, so this is
>> my
>>>> piece of
>>>> code in case any get and idea why is this happening.
>>>>
>>>> http://pastebin.com/Zq88cpwb
>>>>
>>>> Thanks in advance.
>>>> Cheers.
>>>>
>>>> O'car.
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
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