How To Transform A Location-Type Coordinate Into Integer Or String?
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10.5 years ago

I have set of SecRecord objects with SeqFeature.location.start and I want to transform this coordinate into integer to compare to other sets of coordinates, add shifts etc.. How can I do that? I have read Biopython cookbook, but I still can't solve the problem.

biopython • 1.6k views
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In the soon to be released Biopython 1.59 the position objects will be subclasses of int, so you won't need to do anything.

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start = int(str(seqRecord.features[0].location.start))

Well, I converted it first into string, then into integer, is there a more elegant solution?

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Goog idea.thanks!

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can you give more of your code?

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10.5 years ago

I think you need to get the position of the start.

So if currFeat is a SeqFeature from your SeqRecord object:

location = currFeat.location

start = location.start.position

end = location.end.position

start and end should be integers.

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Exactly - although in the soo to be released Biopython 1.59 the position objects will subclass int so you can use them directly.

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