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

Question

[Jelena_bioinf]

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.

[Niallhaslam]

Have you tried nofuzzy_start instead of start?

http://biopython.org/DIST/docs/api/Bio.SeqFeature.FeatureLocation-class.html

[Peter]

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.

[Jelena_bioinf]

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

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

[Jelena_bioinf]

Goog idea.thanks!

[Niek De Klein]

can you give more of your code?

Answer 1

[Niallhaslam]

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.

[Peter]

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

Answer 2

[Asan Emirsale]

I apologize for revealing this ancient thread, but since the discussion is listed among search results for the question, some updates are required. In the current biopython, one should use

start = int(feature.location.start)

The feature.location.start.position is now abandoned as well feature.location.end.position.

Best regards

Asan