[Biopython-dev] [Biopython (old issues only) - Bug #2818] (Resolved) Add start and end properties to SeqFeature object

[redmine at redmine.open-bio.org]

Issue #2818 has been updated by Peter Cock.

Status changed from New to Resolved
% Done changed from 0 to 100

Resolved with changes to Biopython since, including the new CompoundLocation object for joins, and making the position objects more integer like.

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Bug #2818: Add start and end properties to SeqFeature object
https://redmine.open-bio.org/issues/2818#change-15388

* Author: Peter Cock
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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An enhancment proposed on the mailing list would add start and end properties to the SeqFeature returning plain integers (non-fuzzy approximations to the start and end locations) suitable for slicing most parent sequences.  Dealing with a join location would still be tricky.

Example usage:

>>> from Bio import SeqIO
>>> record = SeqIO.read(open("NC_005816.gb"),"gb")
>>> feature = record.features[2]
>>> print feature
type: gene
location: [86:1109]
ref: None:None
strand: 1
qualifiers: 
	Key: db_xref, Value: ['GeneID:2767718']
	Key: locus_tag, Value: ['YP_pPCP01']

>>> record[feature.start:feature.end]
SeqRecord(seq=Seq('ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGCACAAGCAGGGAATG...TGA', IUPACAmbiguousDNA()), id='NC_005816.1', name='NC_005816', description='Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence.', dbxrefs=[])
>>> record.seq[feature.start:feature.end]
Seq('ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGCACAAGCAGGGAATG...TGA', IUPACAmbiguousDNA())

Patch to follow.

---Files--------------------------------
sf_start_end.patch (519 Bytes)


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