error using gmod_bulk_load_gff3.pl

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error using gmod_bulk_load_gff3.pl

anja
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Re: error using gmod_bulk_load_gff3.pl

Bob MacCallum
Hi Anja,
Take a closer look at your gff file - some of your columns are not
delimited by tabs.
cheers,
Bob.

On Thu, Sep 16, 2010 at 12:06 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi all,
>
> I tried to load my data into chado with the gmod_bulk_load_gff3.pl command
> and got this error:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: 'ID=NTR;Name=motif1_tall_e
> ' is not a valid phase
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqFeature::Annotated::phase
> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Annotated.pm:545
> STACK: Bio::FeatureIO::gff::_handle_feature
> /usr/local/share/perl/5.10.1/Bio/FeatureIO/gff.pm:535
> STACK: Bio::FeatureIO::gff::next_feature
> /usr/local/share/perl/5.10.1/Bio/FeatureIO/gff.pm:172
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:775
> -----------------------------------------------------------
>
> I have a couple of motifs specified (a-f for the tall one) but it only
> complains about "e"? I attached my gff file if someone wants to take a look.
> Any help appreciated...
>
> Anja
>

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Re: error using gmod_bulk_load_gff3.pl

anja
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Re: error using gmod_bulk_load_gff3.pl

Bob MacCallum
Sorry, I should have said "in some rows, the columns are not all tab delimited".

Using Linux's "less" command, view the file and then search for the
tab character "/-<tab>-<enter>"
the first problem is on line 46.

On Thu, Sep 16, 2010 at 1:12 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Bob,
>
> I might be blind, but they look fine to me and I delimited by a tab... Which
> columne do you mean?
>
> Cheers,
> Anja
>
> ________________________________
> Date: Thu, 16 Sep 2010 04:50:23 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: error using gmod_bulk_load_gff3.pl
>
> Hi Anja,
> Take a closer look at your gff file - some of your columns are not
> delimited by tabs.
> cheers,
> Bob.
>
> On Thu, Sep 16, 2010 at 12:06 PM, Anja Friedrich
> <[hidden email]> wrote:
>> Hi all,
>>
>> I tried to load my data into chado with the gmod_bulk_load_gff3.pl command
>> and got this error:
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: 'ID=NTR;Name=motif1_tall_e
>> ' is not a valid phase
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
>> STACK: Bio::SeqFeature::Annotated::phase
>> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Annotated.pm:545
>> STACK: Bio::FeatureIO::gff::_handle_feature
>> /usr/local/share/perl/5.10.1/Bio/FeatureIO/gff.pm:535
>> STACK: Bio::FeatureIO::gff::next_feature
>> /usr/local/share/perl/5.10.1/Bio/FeatureIO/gff.pm:172
>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:775
>> -----------------------------------------------------------
>>
>> I have a couple of motifs specified (a-f for the tall one) but it only
>> complains about "e"? I attached my gff file if someone wants to take a
>> look.
>> Any help appreciated...
>>
>> Anja
>>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
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> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
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>

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Re: error using gmod_bulk_load_gff3.pl

anja
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