Re: [GUSDEV] GBParser error

[Thomas O. <ot...@fi...>]

Hi Fabricio,

did you try the insert with another seqeunce? Does the same errors occure?
Looks like, that your genbank entry is not well formated... maybe attach 
it, and I will try to insert it in our DB, without commit. Is it 
NA-Sequence?

Cheers,
Thomas
fab...@de... wrote:

>Hello all,
>
>we are trying to load a genbank file into GUS by GBParser. We downloaded a file
>from NCBI (sequences.gb) as a result search about "tripanosoma cruzi". When we
>executed the command to run the GBParser (ga GUS::Common::Plugin::GBParser
>--file=sequences.gb --gbRel=145.0 --db_rel_id=62 --commit) we got the following
>outputs  on the screen:
>
>...
>ERR     LINE=234512     unparsed line                       
>/locus_tag="SCO7809"
>ERR     LINE=234513     unparsed line                        /note="SC8E7.06,
>possible TetR-family transcriptional
>ERR     LINE=234514     unparsed line                        regulator, len:
>210
>aa. Similar to several other members
>ERR     LINE=234515     unparsed line                        of the TetR-family
>e.g. Streptomyces glaucescens
>ERR     LINE=234516     unparsed line                        SW:TCMR_STRGA
>(EMBL:M80674) tetracenomycin C
>ERR     LINE=234517     unparsed line                        transcriptional
>repressor, TcmR (226 aa), fasta scores
>ERR     LINE=234518     unparsed line                        opt: 187 z-score:
>235.6 E(): 1.2e-05 26.4% identity in 197
>ERR     LINE=234519     unparsed line                        aa overlap and
>Streptomyces coelicolor TR:CAB88457
>ERR     LINE=234520     unparsed line                        (EMBL:AL353815)
>putative TetR-family transcriptional
>...
>and finally this,
>ERR     LINE=235521     unparsed line        RBS            
>complement(8667068..8667073)
>VLD     CBIL::Bio::GenBank::Origin      1
>Tue May  3 15:28:12 2005        STATUS  N=1 ACC=NC_003888       
>TOTAL_OBJECTS=17
>Tue May  3 15:28:35 2005        Genbank entries inserted= 0;  updated= 0; total
>#(inserted::updated::deleted)=17::::
>Tue May  3 15:28:35 2005        FAILURES        Unable to process 2 entries.
>See
>gbparserFailures/
>Tue May  3 15:28:35 2005        RESULT  Genbank entries inserted= 0;  updated=
>0;  failed= 2
>
>In the gbparserFailures/errors file has only this two lines:
>
>------------------ entry number 1 -----------------
>Can't call method "getSingleFeature" on an undefined value at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 311, <GEN0>
>line 379982.
>------------------ entry number 2 -----------------
>Can't call method "getAccession" on an undefined value at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 223, <GEN0>
>line 379983.
>
>Does anyone know what the problem is?
>
>Thanks a lot.
>
>
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