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

[Fidel S. <fi...@vb...>]

Angel,

Thanks.  A day or two works for me.

Fidel


Angel Pizarro <an...@pc...> writes:

     > Fidel,
     > I'll look into this problem. It may take me a bit of time to do so
     > (like a day or two) and get back to you with a full answer.
     > 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
>>
>>
>>