Question: How to interpret the SeqIO.parse record for GenBank features?
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gravatar for jolespin
3.0 years ago by
jolespin120
United States
jolespin120 wrote:

I'm calling these attributes of the feature class: feature.location, feature.type, feature.strand

from the record.features in SeqIO.parse(gbk_file,"genbank")

Output:

[0:6183918](+) source 1
join{[1871:2015](-), [1776:1872](-), [1751:1775](-), [1419:1752](-), [1304:1418](-), [1051:1303](-), [810:1050](-), [722:809](-), [634:721](-), [336:633](-)} CDS -1
[2126:2723](-) CDS -1
[2674:2959](-) CDS -1
[2906:3869](-) CDS -1

I know the (-1) goes with the (-) strand and (1) with the (+) strand.

Is the slice object referencing the (+) strand even when the feature is on the (-) strand? In other words, the 3rd entry, is [2126:2723] on the + strand but the reverse-complement is the feature OR is it in relation to the opposite end of the strand?

Also, what is going on with this join object?

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