[Bioperl-l] Problem with parsing ENSEMBL genbank flat file with genbank2gff3. pls

Babenko, Vladimir (NIH/NLM/NCBI) babenko at ncbi.nlm.nih.gov
Mon Jan 17 14:23:12 EST 2005


    Greetings,
While parsing a genbank file taken from:
ftp://ftp.ensembl.org/pub/current_human/data/flatfiles/genbank/Homo_sapiens.
0.dat as of Jan 2005,
I'm getting the following unflattening error:
--------------------------------------------------------
Processing file /ENSEMBL/Homo_sapiens.0.dat...
working on contig
chromosome:NCBI35:1:1:994676:1...chromosome:NCBI35:1:1:994676:1 Unflattening
error:
Details: 
------------- EXCEPTION  -------------
MSG: PROBLEM, SEVERITY==2
no containers possible for SeqFeature of type: CDS; this SF is being placed
at root level
SF [Bio::SeqFeature::Generic=HASH(0x86485d8)]: CDS; ENSG00000146556

STACK Bio::SeqFeature::Tools::Unflattener::problem
/Bio/SeqFeature/Tools/Unflattener.pm:940
STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/Bio/SeqFeature/Tools/Unflattener.pm:1983
STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/Bio/SeqFeature/Tools/Unflattener.pm:1744
STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/Bio/SeqFeature/Tools/Unflattener.pm:1449
STACK (eval) genbank2gff3.PLS:345
STACK main::unflatten_seq genbank2gff3.PLS:344
STACK toplevel genbank2gff3.PLS:209

--------------------------------------

Possible gene unflattening error withchromosome:NCBI35:1:1:994676:1: consult
STDERR

Using bioperl-1.5.0.RC2 under Linux.

    Would be grateful for the hint,
      Vladimir


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