Re: [Gusdev-gusdev] GBParser failing to insert features

[Steve F. <sfi...@pc...>]

fidel-

can you send us a test file which is the smallest possible file that 
reproduces the problem?

thanks,
steve

Angel Pizarro wrote:

> Fidel,
> In looking at the code and quickly refreshing myself on what is there, 
> I have come to the following conclusions:
>
> Loading of Features are independent. For instance the "gene" and "CDS" 
> features have nothing to do with each other as far as GBParser is 
> concerned.
>
> Both of these entries should be able to be instered, since they have 
> valid attributes or a db_xref .
>
> In short, I do not knopw what the problem is from a cursury look into 
> the inner working of the code. I will need to try to re-create the 
> error here and look at the log output.
>
> Will update you when I have done this.
> Angel
> Fidel Salas wrote:
>
>> I used the GBParser plugin to upload some GenBank entry which contains
>> thousands of features.  However, only 33 features are found in the
>> database.
>>
>> The features found in the database are exemplified by the following
>> two features from the GenBank file:
>>     gene            complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /db_xref="GeneID:1445541"
>>     CDS             complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="saccharopine dehydrogenase"
>>                     /protein_id="NP_147035.1"
>>                     /db_xref="GI:14602185"
>>                     /db_xref="GeneID:1445541"
>>                     
>> /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>>                     
>> LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>>                     
>> DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>>                     
>> RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>>                     
>> GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>>                     
>> DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>>
>>
>> The ones that did not make it in look like this:
>>     gene            complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /db_xref="GeneID:1445602"
>>     CDS             complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="hypothetical protein"
>>                     /protein_id="NP_146894.1"
>>                     /db_xref="GI:14600380"
>>                     /db_xref="GeneID:1445602"
>>                     
>> /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>>                     
>> VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>>                     
>> SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>>                     
>> ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>>                     LLAGVTTLFVVTMLIMINKEGKY"
>>     gene            complement(938..1276)
>>                     /locus_tag="APE0002"
>>                     /db_xref="GeneID:1445577"
>>
>> The one element that is present in the features that are uploaded but
>> absent in those that do not is the gene qualifier.
>>
>> Looking at the schema it is not obvious to me why the gene qualifier
>> needs to be present in a feature in order to be uploaded.  Am I
>> missing something more obvious?
>>
>> Thanks
>>
>> Fidel
>>
>>
>>
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>
>
>
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