[maker-devel] <MAKER Trac Server> #3: dead in Widget::augustus::parse_gene unknown feature type:exon

[MAKER]

#3: dead in Widget::augustus::parse_gene unknown feature type:exon
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  Reporter:  anonymous   |       Owner:        
      Type:  defect      |      Status:  closed
  Priority:  major       |   Milestone:        
 Component:  Code        |     Version:  0.001 
Resolution:  worksforme  |    Keywords:        
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Changes (by carson.genetics.utah.edu):

  * status:  new => closed
  * resolution:  => worksforme

Comment:

 The error is caused by parsing of Augustus output and not by reading the
 hints file.  Augustus output must be parsed and loaded into a
 Bio::Search::Hit::Phathit object in Maker.  For gene predictions this
 object only contains CDS regions.  Raw Augustus ouput does not necessarily
 contain the feature 'exon', since this is redundant with 'CDS' except in
 instances where an exon contains the UTR. When fed the hint 'exonpart',
 Augustus output may start to include 'exon' as a feature.  This feature
 should be ignored by Maker (at least for now) because Maker is only
 concerned about CDS regions in the gene predictions.  Adding 'exon' to the
 if-else statement to force it to be ignored resolves this issue.

 Future consideration may be given to make use of Augustus features outside
 the CDS when building a final gene annotation, but for now Maker uses
 internal code to infer the UTR sequence directly from the ESTs without
 taking this part of the Augustus output into consideration.

 Replying to [ticket:3 anonymous]:
 > Maker crashes when parsing augustus results
 >
 > Error message:
 > ''dead in Widget::augustus::parse_gene unknown feature type:exon''
 >
 > The hints file is being read, but when field[2] is read it doesn't
 support the hint types mentioned in Augustus 2.0: exon, tts, tss (these
 might occur but haven't occurred in my data:: CDSpart, UTR, UTRpart,
 irpart, nonexonpart)
 >
 > Attempts to solve:
 > 1. Added elseif statements to bypass unknown hints. This is problematic
 since without the exon hints I'm unsure if the Augustus results are
 correct or not. I attempted to compare a maker run with Augustus bypassing
 the hints and a maker run without Augustus.
 >
 >
 >
 >
 >
 >
 >

-- 
Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/3#comment:1>
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