« Return to Thread: Problem in loading gff3 files using bp_seqfeature_load.pl
Re: Problem using bp_seqfeature_load.pl
by Scott Cain-4
::
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Hi Arun,
I was thinking that SFStore was using the _rearrange method from
Bio::RootI, but as you pointed out, SFStore is explicitly using the
rearrange method from Bio::DB::GFF::Util::Rearrange (which exports the
rearrange method), so the fact that it can't find it when the load
script is running still indicates that there is a problem.
I'll throw this back out to the entire list: does anybody know what
the problem might be? I currently have a Mac and use SFStore with
Postgres and it works fine (Arun appears to be use a Mac with MySQL).
Generally "reinstall" isn't a solution like it would be with other
operating systems, but it seems that something may have gone wrong
here.
Scott
On Wed, Nov 4, 2009 at 10:18 AM, deepfloyd <arun.to2008@...> wrote:
>
> Hi Scott,
>
> I am using BioPerl 1.6.1 and I installed it using CPAN. There is only one
> instance of BioPerl on my machine. At least when I do sudo find / -name
> Store.pm, I get back a single instance of its occurrence.
>
> The bp_seqfeature_load.pl says "use Bio::DB::GFF::Util::Rearrange" and I
> find Rearrange.pm in this path. If this is the rearrange that it requires
> later, I guess it is looking for it in the right place.
>
> Would you suggest I delete the current version of BioPerl and reinstall?
>
> Thanks
> Arun
>
>
> Scott Cain-4 wrote:
>>
>> Hello,
>>
>> The rearrange method is inherited from somewhere deep within BioPerl
>> (like Bio::Root or the like, I don't remember off hand). If the
>> SeqFeature::Store module can't find it, something is wrong with
>> BioPerl. What version of BioPerl are you using? How did you install
>> it? Could there be more than one instance of BioPerl installed on
>> your system?
>>
>> Scott
>>
>>
>>
>> On Wed, Nov 4, 2009 at 9:13 AM, deepfloyd <arun.to2008@...> wrote:
>>>
>>> Hello,
>>> I am trying to load a gff file into a MySQL database as per the tutorial.
>>> When I try to run bp_seqfeature_load.pl I get the following error.
>>>
>>>
>>> Error Message:
>>> Undefined subroutine &Bio::DB::SeqFeature::Store::rearrange called at
>>> /Library/Perl/5.8.8/Bio/DB/SeqFeature/Store.pm line 351.
>>>
>>> I did not come across any other instances of any one having this error.
>>> It
>>> seems to be like the libraries have a conflict and I have reinstalled
>>> bio-perl. I am still having the same errors. Please let me know if there
>>> is
>>> anything I can do to fix this and thanks a lot for your help in this
>>> regard.
>>>
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26196979.html
>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
> --
> View this message in context: http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26198060.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
I was thinking that SFStore was using the _rearrange method from
Bio::RootI, but as you pointed out, SFStore is explicitly using the
rearrange method from Bio::DB::GFF::Util::Rearrange (which exports the
rearrange method), so the fact that it can't find it when the load
script is running still indicates that there is a problem.
I'll throw this back out to the entire list: does anybody know what
the problem might be? I currently have a Mac and use SFStore with
Postgres and it works fine (Arun appears to be use a Mac with MySQL).
Generally "reinstall" isn't a solution like it would be with other
operating systems, but it seems that something may have gone wrong
here.
Scott
On Wed, Nov 4, 2009 at 10:18 AM, deepfloyd <arun.to2008@...> wrote:
>
> Hi Scott,
>
> I am using BioPerl 1.6.1 and I installed it using CPAN. There is only one
> instance of BioPerl on my machine. At least when I do sudo find / -name
> Store.pm, I get back a single instance of its occurrence.
>
> The bp_seqfeature_load.pl says "use Bio::DB::GFF::Util::Rearrange" and I
> find Rearrange.pm in this path. If this is the rearrange that it requires
> later, I guess it is looking for it in the right place.
>
> Would you suggest I delete the current version of BioPerl and reinstall?
>
> Thanks
> Arun
>
>
> Scott Cain-4 wrote:
>>
>> Hello,
>>
>> The rearrange method is inherited from somewhere deep within BioPerl
>> (like Bio::Root or the like, I don't remember off hand). If the
>> SeqFeature::Store module can't find it, something is wrong with
>> BioPerl. What version of BioPerl are you using? How did you install
>> it? Could there be more than one instance of BioPerl installed on
>> your system?
>>
>> Scott
>>
>>
>>
>> On Wed, Nov 4, 2009 at 9:13 AM, deepfloyd <arun.to2008@...> wrote:
>>>
>>> Hello,
>>> I am trying to load a gff file into a MySQL database as per the tutorial.
>>> When I try to run bp_seqfeature_load.pl I get the following error.
>>>
>>>
>>> Error Message:
>>> Undefined subroutine &Bio::DB::SeqFeature::Store::rearrange called at
>>> /Library/Perl/5.8.8/Bio/DB/SeqFeature/Store.pm line 351.
>>>
>>> I did not come across any other instances of any one having this error.
>>> It
>>> seems to be like the libraries have a conflict and I have reinstalled
>>> bio-perl. I am still having the same errors. Please let me know if there
>>> is
>>> anything I can do to fix this and thanks a lot for your help in this
>>> regard.
>>>
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26196979.html
>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
> --
> View this message in context: http://old.nabble.com/Problem-in-loading-gff3-files-using-bp_seqfeature_load.pl-tp25761770p26198060.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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