[Bioperl-l] genbank2gff3.PLS and the unflatenner - Inconsistent order?

Chad Matsalla chad at dieselwurks.com
Fri Jul 15 15:51:48 EDT 2005


I posted to bioperl-l, hmm, back in June reporting issues with the
genbank2gff* scripts.

Time moved on but I returned to this project where I'm searching through
the Arabidopsis mitochondria for things. I want to gff-i-fy this:

I downloaded the genbank record and ran this command:
$BIOPERL_LIVE/scripts/scripts/Bio-DB-GFF/genbank2gff3.PLS genbank/nc_001284.gb 
Unordered features [on strand:-1]:
NC_001284 Unflattening error:
------------- EXCEPTION  -------------
MSG: ASSERTION ERROR: inconsistent order

Note that I put a BEGIN clause on top of genbank2gff3.PLS script this
morning and cvs committed it. This BEGIN clause ensures that the script
is using the cvs-versions of Bio::* modules which I've compiled into
./blib/lib .

The issue is for more than my mitochondria - it breaks even against test
$BIOPERL/scripts/Bio-DB-GFF/genbank2gff3.PLS $BIOPERL/t/data/test.genbank -o .
L26462 Unflattening error:
...big exception...

Unfortunately, I don't know much about the unflattener but I'll help if
someone can point me in the right direction.

Oh, and just for an additional datapoint, the file
t/data/AE003644_Adh-genomic.gb works.

Thank you,

Chad Matsalla

More information about the Bioperl-l mailing list