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

[Angel P. <an...@pc...>]

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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