[Biopython] iterating over FeatureLocation

[Michael Thon]

Here are two examples from the GenBank format file (not from GenBank though)


     CDS             order(6621..6658,6739..6985)
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_14847-RA:cds"
                     /label=“CDS"

     CDS             419..2374
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_05899-RA:cds"
                     /label=“CDS"

if the feature is a simple feature, then I just need to access its start and end.  If its a compound feature then I need to iterate over each segment, accessing the start and end.

What I am doing at the moment is this:

if feat._sub_features:
	for sf in feat.sub_features:
		start = sf.location.start
		…
else:
	start = feat.location.start
	…

it works, I think.  Is there a better way?

Also, is there an easy way to get the sequence represented by the seqfeature, if it is made up of CompoundLocations?  These features are CDSs where each sub-feature is an exon.  I need to splice them all together and get the translation.

Thanks

On Jan 13, 2014, at 4:38 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Jan 13, 2014 at 3:09 PM, Michael Thon <mike.thon at gmail.com> wrote:
>> I need to iterate over all the features of a sequence, and then
>> iterate over the locations/sublocations in each feature.  I’m not
>> sure how to work with the sublocations though:
>> 
>> I need to do something like this:
>> 
>> for feat in seq.features:
>>        for loc in feat.locations:
>>                start = loc.start
>>                …
>> 
>> which does not work but maybe shows what I need to do.
>> Can anyone help me out?
> 
> Are you talking about join locations? Could you give an example
> (e.g. link to a GenBank file) and what you want to look at?
> 
> Peter
> 
> P.S. This changed a bit back in Biopython 1.62 with the introduction
> of the CompoundLocation object.