[Biopython-dev] SeqFeature.FeatureLocation.extract() silently fails when coordinates are outside of the parent_sequence.

[Kai Blin]

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Hi folks,

I'm currently investigating an error caused by an invalid GenBank file
input that annotates CDS features with invalid coordinates. The
GenBank parser accepts these features, but later my program crashes.

It turns out the crash is because I'm calling the extract() method for
my seq features, which then return an empty Seq object for
out-of-range parent_sequence.

I have the feeling that raising an exception would be the best way of
dealing with this, but of course I can also check the result of
extract() to be different from an empty Seq object.

The line I'd like to throw a ValueError on out-of-bounds coordinates is
https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py#L811

What are your thoughts on this?

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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