gusdev-gusdev

[GUSDEV] ISF InsertSequenceFeatures plugin

[<mro...@cs...>]

Hello GusDev members,

I need you help.....

Using he InsertSequenceFeatures plugin, i loaded the nov 2006 data with NO
problems.

I went to NCBI and found a newer version dec 22 2006

so I unloaded the nov data using the InsertSequenceFeaturesUndo plugin,
and tried to load the dec data getting this error at record 3700:

  In feature map XML file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
  aeruginosa/pa01/genbank2gus.xml' <feature name="CDS"> does not have a
  <qualifier> for 'ribosomal_slippage', which is found in the input.

  Please edit file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
  aeruginosa/pa01/genbank2gus.xml', adding a <qualifer> tag under <feature
  name="CDS">.

  If you want to ignore the input data add <qualifier
  name="ribosomal_slippage" ignore="true"/>.

  If you want to handle the data, you will need to add a special case
  handler (please see the plugin documentation).

So for the moment I modified genbank2gus.xml adding

<qualifier name="ribosomal_slippage" ignore="true"/>


I run InsertSequenceFeaturesUndo with NO problem and then I reloaded the
dec data now getting this error at record 4700:

  ERROR:
  Map XML file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
  aeruginosa/pa01/genbank2gus.xml' does not contain a <feature
  name="pseudogene">, which is found in the input

Lookin into genbank2gus.xml I find that each feature name block has:

<feature name="GC_signal" table="DoTS::DnaRegulatory" so="GC_rich_region">
    <qualifier name="allele" ignore="true"/>
    <qualifier name="citation"/>
    <qualifier name="evidence"/>
    <qualifier name="gene" handler="standard" method="gene"/>
    <qualifier name="label"/>
    <qualifier name="locus_tag" column="source_id"/>
    <qualifier name="map"/>
    <qualifier name="note" handler="standard" method="note"/>
    <qualifier name="old_locus_tag" ignore="true"/>
    <qualifier name="usedin"/>
    <qualifier name="db_xref" handler="standard" method="dbXRef"/>
</feature>


Therefore I need a table name, so, and qualifier names

Could you please tell me where I could find the information needed for the
<feature name="pseudogene"


Thanks

Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
ECS 254
Tel 786-543-3553
email mro...@cs...
Miami, Florida, USA 33199

Re: [GUSDEV] ISF InsertSequenceFeatures plugin

[Steve F. <sfi...@pc...>]

michael-

let's set up a time to have a phone meeting. i think it may be easier to 
help that way.

send me a few times that might work for you next week.

steve

mro...@cs... wrote:
> Hello GusDev members,
>
> I need you help.....
>
> Using he InsertSequenceFeatures plugin, i loaded the nov 2006 data with NO
> problems.
>
> I went to NCBI and found a newer version dec 22 2006
>
> so I unloaded the nov data using the InsertSequenceFeaturesUndo plugin,
> and tried to load the dec data getting this error at record 3700:
>
>   In feature map XML file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
>   aeruginosa/pa01/genbank2gus.xml' <feature name="CDS"> does not have a
>   <qualifier> for 'ribosomal_slippage', which is found in the input.
>
>   Please edit file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
>   aeruginosa/pa01/genbank2gus.xml', adding a <qualifer> tag under <feature
>   name="CDS">.
>
>   If you want to ignore the input data add <qualifier
>   name="ribosomal_slippage" ignore="true"/>.
>
>   If you want to handle the data, you will need to add a special case
>   handler (please see the plugin documentation).
>
> So for the moment I modified genbank2gus.xml adding
>
> <qualifier name="ribosomal_slippage" ignore="true"/>
>
>
> I run InsertSequenceFeaturesUndo with NO problem and then I reloaded the
> dec data now getting this error at record 4700:
>
>   ERROR:
>   Map XML file '/home/biorg-srv-2/mrobi002/gus/pseudomonas
>   aeruginosa/pa01/genbank2gus.xml' does not contain a <feature
>   name="pseudogene">, which is found in the input
>
> Lookin into genbank2gus.xml I find that each feature name block has:
>
> <feature name="GC_signal" table="DoTS::DnaRegulatory" so="GC_rich_region">
>     <qualifier name="allele" ignore="true"/>
>     <qualifier name="citation"/>
>     <qualifier name="evidence"/>
>     <qualifier name="gene" handler="standard" method="gene"/>
>     <qualifier name="label"/>
>     <qualifier name="locus_tag" column="source_id"/>
>     <qualifier name="map"/>
>     <qualifier name="note" handler="standard" method="note"/>
>     <qualifier name="old_locus_tag" ignore="true"/>
>     <qualifier name="usedin"/>
>     <qualifier name="db_xref" handler="standard" method="dbXRef"/>
> </feature>
>
>
> Therefore I need a table name, so, and qualifier names
>
> Could you please tell me where I could find the information needed for the
> <feature name="pseudogene"
>
>
> Thanks
>
> Michael Robinson
> Bioinformatics Research Group (Biorg)
> Florida International University
> ECS 254
> Tel 786-543-3553
> email mro...@cs...
> Miami, Florida, USA 33199
>
>
>
>
>