[BioPython] Genbank LOCUS line slightly misaligned

Peter Saffrey pzs at dcs.gla.ac.uk
Thu Dec 18 13:47:11 UTC 2008


I have a genbank file sent to my lab from a company called Genomatrix. 
It is slightly misformed.

Specifically, the LOCUS lines have the right features, but not quite 
aligned; for example, the "bp" marker is not always at exactly the 
positions ([29:33] and [40:44]) required by _feed_first_line() in 
$biopythonhome/Genbank/Scanner.py.

Have Genomatrix made an error in producing these genbank files, or 
should the bioptyon routines accommodate these variations? Some lines 
just give warnings and plough on, but others report that there isn't a 
space in exactly the right place and fail to read the record at all. I'm 
having to hack the genbank file as we speak...

Thanks,

Peter



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