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Re: [GUSDEV] Question regarding "InsertSequenceFeature"
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From: Steve F. <sfi...@pc...> - 2006-10-05 16:15:30
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kumar- a problem i see is that InsertSequenceFeatures is not designed to do updates. (In GUS/Supported, when a plugin name starts with Insert that means that it only inserts and doesn't update. plugins that insert and/or update start with Load). the reason that ISF doesn't do that is that updating can be tricky. the strategy we have for PlasmoDB is that we just rebuild the whole database, rather than doing updates. steve Kumar, Sanjeev wrote: >Hi Steve, > This date will be used to check whether the same genome sequence has >been updated by genBank or not. > Here my understanding is that whenever genBank changes any old >genomsequence/or its annotations they > change this date. And that comparision we will let me know whether I >need to reload the updated > sequence or not. > What do you think, is it a big change or small change? > >Thanks >Sanjeev > >-----Original Message----- >From: Steve Fischer [mailto:sfi...@pc...] >Sent: Tuesday, October 03, 2006 6:23 PM >To: Kumar, Sanjeev >Cc: gus...@li... >Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature" > >ok, i guess it doesn't. what is it that you are hoping to accomplish? > >steve > >Kumar, Sanjeev wrote: > > >>Hi Steve, >> thanks for your reply. As you suggested I looked into the >>InsertSequenceFeatures.pm code, >> and I found some commnets that says >> # Annotations we haven't used yet >> # SEGMENT segment SimpleValue e.g. " 1 of 2" >> # ORIGIN origin SimpleValue e.g. " X Chromosome" >> # INV date_changed SimpleValue e.g. "08-JUL-1994" >> Other than that I didn't see any where we are reading this >> >> >annotation. > > >>Does this mean that the plugin doesn't read it. >> >>Thanks >>Sanjeev >> >>-----Original Message----- >>From: sfi...@pc... [mailto:sfi...@pc...] >>Sent: Friday, September 29, 2006 6:21 PM >>To: Kumar, Sanjeev >>Cc: gus...@li... >>Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature" >> >>sanjeev- >> >>i believe it does. take a look at the code in the plugin to see if >>you can find where it is parsing that line. >> >>steve >> >>Quoting "Kumar, Sanjeev" <San...@ng...>: >> >> >> >> >>>Hi Group, >>> I have a question regarding InsertSequenceFeature plugin. >>> Following are the first few lines of NCBI genBank genome sequence >>>file: >>>******************************* >>> LOCUS AB255391 978 bp RNA linear >>>VRL 22-JUN-2006 >>> DEFINITION Influenza A virus (A/Aichi/17/2006(H1N1)) gene for >>>hemagglutinin, >>> partial cds. >>> ACCESSION AB255391 >>> VERSION AB255391.1 GI:109452180 >>> KEYWORDS . >>> . >>> . >>>************************* >>>My question is does the plugin parses and store the date shown in >>>first line above (22-JUN-2006). >>>I tried to look in various dbref table but no luck. >>> >>>Any help will be appreciated. >>> >>>Thanks >>>Sanjeev >>> >>>--------------------------------------------------------------------- >>>- >>>--- Take Surveys. Earn Cash. Influence the Future of IT Join >>>SourceForge.net's Techsay panel and you'll get the chance to share >>>your opinions on IT & business topics through brief surveys -- and >>>earn cash >>>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DE >>>V DEV _______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> >> >> >> >> > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
