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Re: GBrowse Search input

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Re: GBrowse Search input

Lincoln Stein
Hi,

I cannot reproduce this problem, so I suspect it is a configuration issue on your end. Unfortunately I can't devote much time to tracking this down due to grant deadlines, and so I'm forwarding your issue to the GMOD mailing list. Hopefully somebody there will be able to help you out sooner.

Lincoln

On Tue, Apr 24, 2012 at 6:48 AM, Chanaka Mannapperuma <[hidden email]> wrote:
Dear Lincoln,

I am using Generic Genome Browser version 2.43 version,
Thanks for quick reply,

truly,
/Chanaka

Hi,

Tell me which version of GBrowse you are using!

Lincoln

On Tue, Apr 24, 2012 at 5:54 AM, <[hidden email]> wrote:
Dear Lincoln,

I was trying to fix GBrowse search problem since several days.
Because GBrowse search only for names(not IDs),when duplicate names exsist in the database GBrowse will not find anything.I just end up with the blank page.I use -debug option but  I cant see any Apache error logs.I also tried different search options but non of them fix the issue.Therefore we cant have duplicate names(Name=) in the GFF file.Which is smilar to ID=Name.Is this GBrowse bug? Is that possible to configure Id as a second search option.my problem is almost similar to this issue http://gmod.827538.n3.nabble.com/Entering-GenBank-Refseq-file-fail-to-display-in-GBrowse2-td944349.html#a966261

here is example of gff file

scaffold_276160 sitka   gene    11414   11956   .       -       .       ID=WS0279_J18.path1;Name=WS0279_J18
scaffold_276160 sitka   mRNA    11414   11956   .       -       .       ID=WS0279_J18.mrna1;Name=WS0279_J18;Parent=WS0279_J18.path1;Coverage=72.4;Identity=99.4
scaffold_276160 sitka   exon    11414   11956   99      -       .       ID=WS0279_J18.mrna1.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18 5 547 +
scaffold_276160 sitka   CDS     11485   11892   99      -       0       ID=WS0279_J18.mrna1.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18 69 476 +
scaffold_276160 sitka   gene    11272   11374   .       -       .       ID=WS0279_J18.path2;Name=WS0279_J18
scaffold_276160 sitka   mRNA    11272   11374   .       -       .       ID=WS0279_J18.mrna2;Name=WS0279_J18;Parent=WS0279_J18.path2;Coverage=15.9;Identity=98.1
scaffold_276160 sitka   exon    11272   11374   98      -       .       ID=WS0279_J18.mrna2.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18 541 642 +
scaffold_276160 sitka   CDS     11339   11374   100     -       0       ID=WS0279_J18.mrna2.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18 541 576 +
scaffold_276160 sitka   CDS     11272   11337   98      -       0       ID=WS0279_J18.mrna2.cds2;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18 577 642 +


Appreciate your help,
/Chan



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: GBrowse Search input

Scott Cain
Hi Chanaka,

Can you please send your configuration file too?  What you are
describing certainly should work.

Scott


On Thu, Apr 26, 2012 at 11:31 AM, Lincoln Stein <[hidden email]> wrote:

> Hi,
>
> I cannot reproduce this problem, so I suspect it is a configuration issue on
> your end. Unfortunately I can't devote much time to tracking this down due
> to grant deadlines, and so I'm forwarding your issue to the GMOD mailing
> list. Hopefully somebody there will be able to help you out sooner.
>
> Lincoln
>
> On Tue, Apr 24, 2012 at 6:48 AM, Chanaka Mannapperuma <[hidden email]>
> wrote:
>>
>> Dear Lincoln,
>>
>> I am using Generic Genome Browser version 2.43 version,
>> Thanks for quick reply,
>>
>> truly,
>> /Chanaka
>>
>> Hi,
>>
>> Tell me which version of GBrowse you are using!
>>
>> Lincoln
>>
>> On Tue, Apr 24, 2012 at 5:54 AM, <[hidden email]> wrote:
>>>
>>> Dear Lincoln,
>>>
>>> I was trying to fix GBrowse search problem since several days.
>>> Because GBrowse search only for names(not IDs),when duplicate names
>>> exsist in the database GBrowse will not find anything.I just end up with the
>>> blank page.I use -debug option but  I cant see any Apache error logs.I also
>>> tried different search options but non of them fix the issue.Therefore we
>>> cant have duplicate names(Name=) in the GFF file.Which is smilar to
>>> ID=Name.Is this GBrowse bug? Is that possible to configure Id as a second
>>> search option.my problem is almost similar to this
>>> issue http://gmod.827538.n3.nabble.com/Entering-GenBank-Refseq-file-fail-to-display-in-GBrowse2-td944349.html#a966261
>>>
>>> here is example of gff file
>>>
>>> scaffold_276160 sitka   gene    11414   11956   .       -       .
>>> ID=WS0279_J18.path1;Name=WS0279_J18
>>> scaffold_276160 sitka   mRNA    11414   11956   .       -       .
>>> ID=WS0279_J18.mrna1;Name=WS0279_J18;Parent=WS0279_J18.path1;Coverage=72.4;Identity=99.4
>>> scaffold_276160 sitka   exon    11414   11956   99      -       .
>>> ID=WS0279_J18.mrna1.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>>> 5 547 +
>>> scaffold_276160 sitka   CDS     11485   11892   99      -       0
>>> ID=WS0279_J18.mrna1.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>>> 69 476 +
>>> scaffold_276160 sitka   gene    11272   11374   .       -       .
>>> ID=WS0279_J18.path2;Name=WS0279_J18
>>> scaffold_276160 sitka   mRNA    11272   11374   .       -       .
>>> ID=WS0279_J18.mrna2;Name=WS0279_J18;Parent=WS0279_J18.path2;Coverage=15.9;Identity=98.1
>>> scaffold_276160 sitka   exon    11272   11374   98      -       .
>>> ID=WS0279_J18.mrna2.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 541 642 +
>>> scaffold_276160 sitka   CDS     11339   11374   100     -       0
>>> ID=WS0279_J18.mrna2.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 541 576 +
>>> scaffold_276160 sitka   CDS     11272   11337   98      -       0
>>> ID=WS0279_J18.mrna2.cds2;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 577 642 +
>>>
>>>
>>> Appreciate your help,
>>> /Chan
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> 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

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: GBrowse Search input

Chanaka
Hi Scott,

here I have attached the configuration files.please email me if you need more information regarding issue.

/Chanaka


On Thu, Apr 26, 2012 at 5:47 PM, Scott Cain <[hidden email]> wrote:
Hi Chanaka,

Can you please send your configuration file too?  What you are
describing certainly should work.

Scott


On Thu, Apr 26, 2012 at 11:31 AM, Lincoln Stein <[hidden email]> wrote:
> Hi,
>
> I cannot reproduce this problem, so I suspect it is a configuration issue on
> your end. Unfortunately I can't devote much time to tracking this down due
> to grant deadlines, and so I'm forwarding your issue to the GMOD mailing
> list. Hopefully somebody there will be able to help you out sooner.
>
> Lincoln
>
> On Tue, Apr 24, 2012 at 6:48 AM, Chanaka Mannapperuma <[hidden email]>
> wrote:
>>
>> Dear Lincoln,
>>
>> I am using Generic Genome Browser version 2.43 version,
>> Thanks for quick reply,
>>
>> truly,
>> /Chanaka
>>
>> Hi,
>>
>> Tell me which version of GBrowse you are using!
>>
>> Lincoln
>>
>> On Tue, Apr 24, 2012 at 5:54 AM, <[hidden email]> wrote:
>>>
>>> Dear Lincoln,
>>>
>>> I was trying to fix GBrowse search problem since several days.
>>> Because GBrowse search only for names(not IDs),when duplicate names
>>> exsist in the database GBrowse will not find anything.I just end up with the
>>> blank page.I use -debug option but  I cant see any Apache error logs.I also
>>> tried different search options but non of them fix the issue.Therefore we
>>> cant have duplicate names(Name=) in the GFF file.Which is smilar to
>>> ID=Name.Is this GBrowse bug? Is that possible to configure Id as a second
>>> search option.my problem is almost similar to this
>>> issue http://gmod.827538.n3.nabble.com/Entering-GenBank-Refseq-file-fail-to-display-in-GBrowse2-td944349.html#a966261
>>>
>>> here is example of gff file
>>>
>>> scaffold_276160 sitka   gene    11414   11956   .       -       .
>>> ID=WS0279_J18.path1;Name=WS0279_J18
>>> scaffold_276160 sitka   mRNA    11414   11956   .       -       .
>>> ID=WS0279_J18.mrna1;Name=WS0279_J18;Parent=WS0279_J18.path1;Coverage=72.4;Identity=99.4
>>> scaffold_276160 sitka   exon    11414   11956   99      -       .
>>> ID=WS0279_J18.mrna1.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>>> 5 547 +
>>> scaffold_276160 sitka   CDS     11485   11892   99      -       0
>>> ID=WS0279_J18.mrna1.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>>> 69 476 +
>>> scaffold_276160 sitka   gene    11272   11374   .       -       .
>>> ID=WS0279_J18.path2;Name=WS0279_J18
>>> scaffold_276160 sitka   mRNA    11272   11374   .       -       .
>>> ID=WS0279_J18.mrna2;Name=WS0279_J18;Parent=WS0279_J18.path2;Coverage=15.9;Identity=98.1
>>> scaffold_276160 sitka   exon    11272   11374   98      -       .
>>> ID=WS0279_J18.mrna2.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 541 642 +
>>> scaffold_276160 sitka   CDS     11339   11374   100     -       0
>>> ID=WS0279_J18.mrna2.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 541 576 +
>>> scaffold_276160 sitka   CDS     11272   11337   98      -       0
>>> ID=WS0279_J18.mrna2.cds2;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>>> 577 642 +
>>>
>>>
>>> Appreciate your help,
>>> /Chan
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> 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


------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Re: GBrowse Search input

Scott Cain
Hi Chanaka,

I'd like to come as close to possible in recreating your problem.  Can
you send me GFF files that demonstrate the problem?

Thanks,
Scott


On Thu, Apr 26, 2012 at 12:01 PM, Chanaka Mannapperuma <[hidden email]> wrote:

> Hi Scott,
>
> here I have attached the configuration files.please email me if you need
> more information regarding issue.
>
> /Chanaka
>
>
> On Thu, Apr 26, 2012 at 5:47 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Chanaka,
>>
>> Can you please send your configuration file too?  What you are
>> describing certainly should work.
>>
>> Scott
>>
>>
>> On Thu, Apr 26, 2012 at 11:31 AM, Lincoln Stein <[hidden email]>
>> wrote:
>> > Hi,
>> >
>> > I cannot reproduce this problem, so I suspect it is a configuration
>> > issue on
>> > your end. Unfortunately I can't devote much time to tracking this down
>> > due
>> > to grant deadlines, and so I'm forwarding your issue to the GMOD mailing
>> > list. Hopefully somebody there will be able to help you out sooner.
>> >
>> > Lincoln
>> >
>> > On Tue, Apr 24, 2012 at 6:48 AM, Chanaka Mannapperuma <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Lincoln,
>> >>
>> >> I am using Generic Genome Browser version 2.43 version,
>> >> Thanks for quick reply,
>> >>
>> >> truly,
>> >> /Chanaka
>> >>
>> >> Hi,
>> >>
>> >> Tell me which version of GBrowse you are using!
>> >>
>> >> Lincoln
>> >>
>> >> On Tue, Apr 24, 2012 at 5:54 AM, <[hidden email]> wrote:
>> >>>
>> >>> Dear Lincoln,
>> >>>
>> >>> I was trying to fix GBrowse search problem since several days.
>> >>> Because GBrowse search only for names(not IDs),when duplicate names
>> >>> exsist in the database GBrowse will not find anything.I just end up
>> >>> with the
>> >>> blank page.I use -debug option but  I cant see any Apache error logs.I
>> >>> also
>> >>> tried different search options but non of them fix the issue.Therefore
>> >>> we
>> >>> cant have duplicate names(Name=) in the GFF file.Which is smilar to
>> >>> ID=Name.Is this GBrowse bug? Is that possible to configure Id as a
>> >>> second
>> >>> search option.my problem is almost similar to this
>> >>>
>> >>> issue http://gmod.827538.n3.nabble.com/Entering-GenBank-Refseq-file-fail-to-display-in-GBrowse2-td944349.html#a966261
>> >>>
>> >>> here is example of gff file
>> >>>
>> >>> scaffold_276160 sitka   gene    11414   11956   .       -       .
>> >>> ID=WS0279_J18.path1;Name=WS0279_J18
>> >>> scaffold_276160 sitka   mRNA    11414   11956   .       -       .
>> >>>
>> >>> ID=WS0279_J18.mrna1;Name=WS0279_J18;Parent=WS0279_J18.path1;Coverage=72.4;Identity=99.4
>> >>> scaffold_276160 sitka   exon    11414   11956   99      -       .
>> >>>
>> >>> ID=WS0279_J18.mrna1.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>> >>> 5 547 +
>> >>> scaffold_276160 sitka   CDS     11485   11892   99      -       0
>> >>>
>> >>> ID=WS0279_J18.mrna1.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>> >>> 69 476 +
>> >>> scaffold_276160 sitka   gene    11272   11374   .       -       .
>> >>> ID=WS0279_J18.path2;Name=WS0279_J18
>> >>> scaffold_276160 sitka   mRNA    11272   11374   .       -       .
>> >>>
>> >>> ID=WS0279_J18.mrna2;Name=WS0279_J18;Parent=WS0279_J18.path2;Coverage=15.9;Identity=98.1
>> >>> scaffold_276160 sitka   exon    11272   11374   98      -       .
>> >>>
>> >>> ID=WS0279_J18.mrna2.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 541 642 +
>> >>> scaffold_276160 sitka   CDS     11339   11374   100     -       0
>> >>>
>> >>> ID=WS0279_J18.mrna2.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 541 576 +
>> >>> scaffold_276160 sitka   CDS     11272   11337   98      -       0
>> >>>
>> >>> ID=WS0279_J18.mrna2.cds2;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 577 642 +
>> >>>
>> >>>
>> >>> Appreciate your help,
>> >>> /Chan
>> >
>> >
>> >
>> >
>> > --
>> > Lincoln D. Stein
>> > Director, Informatics and Biocomputing Platform
>> > Ontario Institute for Cancer Research
>> > 101 College St., Suite 800
>> > Toronto, ON, Canada M5G0A3
>> > 416 673-8514
>> > Assistant: Renata Musa <[hidden email]>
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Live Security Virtual Conference
>> > Exclusive live event will cover all the ways today's security and
>> > threat landscape has changed and how IT managers can respond.
>> > Discussions
>> > will include endpoint security, mobile security and the latest in
>> > malware
>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > 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
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: GBrowse Search input

Chanaka
Hi Scott,

I use following sample it will search for gene_1.path1 perfect.

Sample1

scaffold_1      poplar  gene    12632   13612   .       +       .       ID=gene_1.1;Name=gene_1.path1

scaffold_1      poplar  gene    22190   22516   .       +       .       ID=gene_1.2;Name=gene_1.path1

scaffold_1      poplar  gene    74076   75893   .       +       .       ID=gene_1.3;Name=gene_2.path1

scaffold_1      poplar  gene    80207   81289   .       -       .       ID=gene_1.4;Name=gene_2.path1

scaffold_1      poplar  gene    105028  107984  .       +       .       ID=gene_1.5;Name=gene_2.path1

scaffold_1      poplar  gene    112882  116932  .       -       .       ID=gene_1.6;Name=gene_3.path1

scaffold_1      poplar  gene    127945  132456  .       -       .       ID=gene_1.7;Name=gene_3.path1

scaffold_1      poplar  gene    137068  139439  .       -       .       ID=gene_1.8;Name=gene_3.path1

scaffold_1      poplar  gene    140803  141195  .       -       .       ID=gene_1.9;Name=gene_3.path1

scaffold_1      poplar  gene    163852  164909  .       -       .       ID=gene_1.10;Name=gene_4.path1


I used following gff3 sample then I can see the GBrowse results for WS0279_J18,I confused because following pattern include duplicate IDs but  it loaded to mysql databse without an exception (bp_seqfeature_load.pl).

 Sample2

scaffold_1      sitka   gene    30      48      .       +       .       ID=WS.path1;Name=WS02724_O12

scaffold_1      sitka   gene    110     119     .       -       .       ID=WS.path1;Name=WS0279_J18

scaffold_1      sitka   gene    207     223     .       -       .       ID=WS.path2;Name=WS0279_J18


but If I use following gff3 sample I can’t get results for  WS0279_J18.I just get the blank page, Did I do something wrong?

Sample3

scaffold_1      sitka   gene    30      48      .       +       .       ID=WS02724_O12.path1;Name=WS02724_O12

scaffold_1      sitka   gene    110     119     .       -       .       ID=WS0279_J18.path1;Name=WS0279_J18

scaffold_1      sitka   gene    207     223     .       -       .       ID=WS0279_J18.path2;Name=WS0279_J18


thanks,

/Chanaka


On Fri, Apr 27, 2012 at 5:19 PM, Scott Cain <[hidden email]> wrote:
Hi Chanaka,

I'd like to come as close to possible in recreating your problem.  Can
you send me GFF files that demonstrate the problem?

Thanks,
Scott


On Thu, Apr 26, 2012 at 12:01 PM, Chanaka Mannapperuma <[hidden email]> wrote:
> Hi Scott,
>
> here I have attached the configuration files.please email me if you need
> more information regarding issue.
>
> /Chanaka
>
>
> On Thu, Apr 26, 2012 at 5:47 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Chanaka,
>>
>> Can you please send your configuration file too?  What you are
>> describing certainly should work.
>>
>> Scott
>>
>>
>> On Thu, Apr 26, 2012 at 11:31 AM, Lincoln Stein <[hidden email]>
>> wrote:
>> > Hi,
>> >
>> > I cannot reproduce this problem, so I suspect it is a configuration
>> > issue on
>> > your end. Unfortunately I can't devote much time to tracking this down
>> > due
>> > to grant deadlines, and so I'm forwarding your issue to the GMOD mailing
>> > list. Hopefully somebody there will be able to help you out sooner.
>> >
>> > Lincoln
>> >
>> > On Tue, Apr 24, 2012 at 6:48 AM, Chanaka Mannapperuma <[hidden email]>
>> > wrote:
>> >>
>> >> Dear Lincoln,
>> >>
>> >> I am using Generic Genome Browser version 2.43 version,
>> >> Thanks for quick reply,
>> >>
>> >> truly,
>> >> /Chanaka
>> >>
>> >> Hi,
>> >>
>> >> Tell me which version of GBrowse you are using!
>> >>
>> >> Lincoln
>> >>
>> >> On Tue, Apr 24, 2012 at 5:54 AM, <[hidden email]> wrote:
>> >>>
>> >>> Dear Lincoln,
>> >>>
>> >>> I was trying to fix GBrowse search problem since several days.
>> >>> Because GBrowse search only for names(not IDs),when duplicate names
>> >>> exsist in the database GBrowse will not find anything.I just end up
>> >>> with the
>> >>> blank page.I use -debug option but  I cant see any Apache error logs.I
>> >>> also
>> >>> tried different search options but non of them fix the issue.Therefore
>> >>> we
>> >>> cant have duplicate names(Name=) in the GFF file.Which is smilar to
>> >>> ID=Name.Is this GBrowse bug? Is that possible to configure Id as a
>> >>> second
>> >>> search option.my problem is almost similar to this
>> >>>
>> >>> issue http://gmod.827538.n3.nabble.com/Entering-GenBank-Refseq-file-fail-to-display-in-GBrowse2-td944349.html#a966261
>> >>>
>> >>> here is example of gff file
>> >>>
>> >>> scaffold_276160 sitka   gene    11414   11956   .       -       .
>> >>> ID=WS0279_J18.path1;Name=WS0279_J18
>> >>> scaffold_276160 sitka   mRNA    11414   11956   .       -       .
>> >>>
>> >>> ID=WS0279_J18.mrna1;Name=WS0279_J18;Parent=WS0279_J18.path1;Coverage=72.4;Identity=99.4
>> >>> scaffold_276160 sitka   exon    11414   11956   99      -       .
>> >>>
>> >>> ID=WS0279_J18.mrna1.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>> >>> 5 547 +
>> >>> scaffold_276160 sitka   CDS     11485   11892   99      -       0
>> >>>
>> >>> ID=WS0279_J18.mrna1.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna1;Target=WS0279_J18
>> >>> 69 476 +
>> >>> scaffold_276160 sitka   gene    11272   11374   .       -       .
>> >>> ID=WS0279_J18.path2;Name=WS0279_J18
>> >>> scaffold_276160 sitka   mRNA    11272   11374   .       -       .
>> >>>
>> >>> ID=WS0279_J18.mrna2;Name=WS0279_J18;Parent=WS0279_J18.path2;Coverage=15.9;Identity=98.1
>> >>> scaffold_276160 sitka   exon    11272   11374   98      -       .
>> >>>
>> >>> ID=WS0279_J18.mrna2.exon1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 541 642 +
>> >>> scaffold_276160 sitka   CDS     11339   11374   100     -       0
>> >>>
>> >>> ID=WS0279_J18.mrna2.cds1;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 541 576 +
>> >>> scaffold_276160 sitka   CDS     11272   11337   98      -       0
>> >>>
>> >>> ID=WS0279_J18.mrna2.cds2;Name=WS0279_J18;Parent=WS0279_J18.mrna2;Target=WS0279_J18
>> >>> 577 642 +
>> >>>
>> >>>
>> >>> Appreciate your help,
>> >>> /Chan
>> >
>> >
>> >
>> >
>> > --
>> > Lincoln D. Stein
>> > Director, Informatics and Biocomputing Platform
>> > Ontario Institute for Cancer Research
>> > 101 College St., Suite 800
>> > Toronto, ON, Canada M5G0A3
>> > 416 673-8514
>> > Assistant: Renata Musa <[hidden email]>
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Live Security Virtual Conference
>> > Exclusive live event will cover all the ways today's security and
>> > threat landscape has changed and how IT managers can respond.
>> > Discussions
>> > will include endpoint security, mobile security and the latest in
>> > malware
>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > 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
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: GBrowse Search input

Chanaka
Hi,

I still have problem with GBrowse search input .here is my issue:I think it has issue with duplicate names, underscore (_ ) or dots (.) For example if it contains duplicate names it returns blank page.
Sample2
scaffold_1      sitka   gene    30      48      .       +       .       ID=WS.path1;Name=WS02724_O12
scaffold_1      sitka   gene    110     119     .       -       .       ID=WS.path1;Name=WS0279_J18
scaffold_1      sitka   gene    207     223     .       -       .       ID=WS.path2;Name=WS0279_J18


Sample 1 it contains duplicate IDs but it will not return an exception(I used "perl bp_seqfeature_load.pl -p [pass] -u [name] -d [db]  -c -f [file]" gff3 file stored into database) and it works as expected:
Sample 1
scaffold_1      sitka   gene    30      48      .       +       .       ID=PS.path1;Name=PS02724O12
scaffold_1      sitka   gene    110     119     .       -       .       ID=PS.path1;Name=PS0279J18
scaffold_1      sitka   gene    207     223     .       -       .       ID=PS.path2;Name=PS0279J18


Sample3
scaffold_1      sitka   gene    30      48      .       +       .       ID=WS02724_O12.path1;Name=WS02724_O12
scaffold_1      sitka   gene    110     119     .       -       .       ID=WS0279_J18.path1;Name=WS0279_J18
scaffold_1      sitka   gene    207     223     .       -       .       ID=WS0279_J18.path2;Name=WS0279_J18


Problem is we can see results for PS02724O12  but not for WS02724_O12 even we have duplicate ids. I tried with debug option and different database search options like all (wildcard,autocomplete..).Is this bug with GBrowse or did I do something wrong.I reported this issue last April but still no luck.

thanks,
/Chanaka



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Re: GBrowse Search input

Chanaka
Hi,

FInally I fixed this issue, its not bug with GBrowse (may be validation issue because its not complaining). I had issue with BioPerl and Bio::Graphics module.I used following commands and then resintall Bio Graphics module.
sudo apt-get remove libgd-gd2-perl
sudo apt-get install libgd2-noxpm-dev
sudo perl -MCPAN -e 'install GD'

Installed Bio Graphics using CPAN (wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-Graphics-2.31.tar.gz). I hope this helps to someone with same issue.

/Chanaka


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