[Biopython] How to use SeqRecord to get the subseq location information

Wibowo Arindrarto w.arindrarto at gmail.com
Fri May 4 06:09:31 UTC 2012


Hi Liu,

It looks like the problem is caused by the values you put in your
SeqFeature. Your sequence length is less than the feature location
values. If you try plugging in a number in range, like this:

>>> example_feature = SeqFeature(FeatureLocation(5, 7), type="mRNA", strand=-1)

You should still keep the feature in your subsequence, like so:

>>> subseq = simple_seq_r[3:10]
>>> subseq.features
[SeqFeature(FeatureLocation(ExactPosition(2), ExactPosition(4),
strand=-1), type='mRNA')]

Hope that helps :),

cheers,
Bow



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