[Biopython-dev] Nice small test case for fuzzy locations

Peter peter at maubp.freeserve.co.uk
Wed Apr 22 11:00:19 UTC 2009


Hi all,

This is a nice small GenBank file with fuzzy locations, joins, and fuzzy joins:
ftp://ftp.ncbi.nih.gov/genomes/Protozoa/Cryptosporidium_parvum/NC_006980.gbk

I think this will make an excellent test case, see new unittest based
Tests/test_SeqIO_feature.py which we can extend to include GFF or PTT
files when they are in Bio.SeqIO too.  The good news is our non-fuzzy
locations appear to be doing just what GenBank does - you did a good
job there Brad :)

If anyone comes across a better example file let us know (i.e. also
very small, but with between positions, one of position etc as well).

Peter



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