[Biopython] Edit feature's location

[Ilya Flyamer]

Dear Peter,

Thank you very much, this seems to be exactly what I was looking for.

Best,
Ilya


2014-07-28 11:09 GMT+02:00 Peter Cock <p.j.a.cock at googlemail.com>:

> On Fri, Jul 25, 2014 at 1:55 PM, Ilya Flyamer <flyamer at gmail.com> wrote:
> > Hi,
> >
> > is there a way to either change SeqFeature's location in place or create
> a
> > copy with a different location? Assigning to feature.location.start
> raises
> > an AttributeError.
>
> The FeatureLocation properties are (currently at least) read only
> attributes. You could replace the current SeqFeature's location
> with a new FeatureLocation instead:
>
> Example to get a SeqFeature,
>
> >>> from Bio import SeqIO
> >>> record = SeqIO.read("NC_000932.g", "genbank")
> >>> f = record.features[10]
> >>> f
> SeqFeature(FeatureLocation(ExactPosition(2055), ExactPosition(3570),
> strand=-1), type='CDS')
> >>> print f
> type: CDS
> location: [2055:3570](-)
> qualifiers:
>     Key: codon_start, Value: ['1']
>     Key: db_xref, Value: ['GI:126022795', 'GeneID:844797']
>     Key: gene, Value: ['matK']
>     Key: locus_tag, Value: ['ArthCp003']
>     Key: product, Value: ['maturase K']
>     Key: protein_id, Value: ['NP_051040.2']
>     Key: transl_table, Value: ['11']
>     Key: translation, Value:
>
> ['MDKFQGYLEFDGARQQSFLYPLFFREYIYVLAYDHGLNRLNRNRYIFLENADYDKKYSSLITKRLILRMYEQNRLIIPTKDVNQNSFLGHTSLFYYQMISVLFAVIVEIPFSLRLGSSFQGKQLKKSYNLQSIHSIFPFLEDKLGHFNYVLDVLIPYPIHLEILVQTLRYRVKDASSLHFFRFCLYEYCNWKNFYIKKKSILNPRFFLFLYNSHVCEYESIFFFLRKRSSHLRSTSYEVLFERIVFYGKIHHFFKVFVNNFPAILGLLKDPFIHYVRYHGRCILATKDTPLLMNKWKYYFVNLWQCYFSVWFQSQKVNINQLSKDNLEFLGYLSSLRLNPLVVRSQMLENSFLIDNVRIKLDSKIPISSIIGSLAKDKFCNVLGHPISKATWTDSSDSDILNRFVRICRNISHYYSGSSKKKNLYRIKYILRLCCVKTLARKHKSTVRTFLKRLGSGLLEEFLTGEDQVLSLIFPRSYYASKRLYRVRIWYLDILYLNDLVNHE']
> >>> f.location
> FeatureLocation(ExactPosition(2055), ExactPosition(3570), strand=-1)
> >>> print f.location
> [2055:3570](-)
>
> Now let's change the location:
>
> >>> from Bio.SeqFeature import FeatureLocation
> >>> f.location = FeatureLocation(2049, 3570, strand=-1)
> >>> f.location
> FeatureLocation(ExactPosition(2049), ExactPosition(3570), strand=-1)
> >>> print f.location
> [2049:3570](-)
>
> > My ultimate goal is to move all features in a genbank file by some
> specific
> > number of nucleotides (for example, add 1000 to all coordinates). If
> someone
> > can help me and tell about an easier way, I will appreciate it.
>
> The easy way is just to add 1000 to the feature location, which will give
> you a new FeatureLocation with shifted coordinates:
>
> >>> loc = FeatureLocation(2049, 3564, strand=-1)
> >>> loc
> FeatureLocation(ExactPosition(2049), ExactPosition(3564), strand=-1)
> >>> loc + 6
> FeatureLocation(ExactPosition(2055), ExactPosition(3570), strand=-1)
>
> On in situ, replacing the old FeatureLocation object:
>
> >>> loc += 6
> >>> loc
> FeatureLocation(ExactPosition(2055), ExactPosition(3570), strand=-1)
>
> Also, you might have missed this kind of thing in the tutorial - adding
> to a SeqRecord will adjust the feature locations accordingly:
>
> >>> from Bio import SeqIO
> >>> record = SeqIO.read("NC_000932.gb", "genbank")
> >>> record.features[10].location
> FeatureLocation(ExactPosition(2055), ExactPosition(3570), strand=-1)
> >>> new = "N"*1000 + record
> >>> new.features[10].location
> FeatureLocation(ExactPosition(3055), ExactPosition(4570), strand=-1)
>
> See also "Adding SeqRecord objects" in the Tutorial:
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
>
> Peter
>
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