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Re: [GUSDEV] Question regarding "InsertSequenceFeature"
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From: Kumar, S. <San...@ng...> - 2006-10-05 16:22:00
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Hi Steve,
You are absolutely right. That is Why I am going to right small perl
program to parse each genome sequence to be loaded to get the date and
accession, and then I will search in the database to see whether the
accession exists in the "nasequenceimp" table or not. If accession
doesn't exists then it will be considered as a new load and if exists
the we will compare the date (which we are talking about), if the new
file's date is later, then we will delete the old sequence and load the
updated sequence.
This way we will save "lot of data processing time".
Since, we are dealing with Flu sequences we have total count of more
than 38000 sequences and with so many numbers I felt it will be time
consuming to rebuild the whole database.
Thanks
Sanjeev
-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Thursday, October 05, 2006 12:15 PM
To: Kumar, Sanjeev
Cc: gus...@li...
Subject: Re: [GUSDEV] Question regarding "InsertSequenceFeature"
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=20
>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?=20
>
>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:
> =20
>
>>Hi Steve,
>> thanks for your reply. As you suggested I looked into the=20
>>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
>> =20
>>
>annotation.
> =20
>
>>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=20
>>you can find where it is parsing that line.
>>
>>steve
>>
>>Quoting "Kumar, Sanjeev" <San...@ng...>:
>>
>> =20
>> =20
>>
>>>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=20
>>>first line above (22-JUN-2006).
>>>I tried to look in various dbref table but no luck.
>>>
>>>Any help will be appreciated.
>>>
>>>Thanks
>>>Sanjeev
>>>
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>>
>> =20
>> =20
>>
>
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