[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