[Bioperl-l] load_seqdatabase error with a specific locus from genbank

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Apr 6 21:05:25 EDT 2009


> The full record is here: http://www.ncbi.nlm.nih.gov/nuccore/544772

  gene            order(S67862.1:72..75,join(S67863.1:1..788,1..19))

> Does anyone see why the location parser should have a problem with the first
> gene feature? It's nested, and has remote location components, but at first
> sight nothing jumps out at me as extraordinary. Has someone recently changed
> the location parsing code? If no-one has an immediate idea what could be at
> work here, this needs investigating.

I'm not sure if Bioperl handles the order() operator?

For those unfamilair with the order() operator:

http://www.ncbi.nlm.nih.gov/collab/FT/#3.5.2

order(location,location, ... location)
The elements can be found in the specified order (5' to 3' direction),
but nothing is implied about the reasonableness about joining them.


--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA


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