[Biopython-dev] [Bug 2818] New: Add start and end properties to SeqFeature object

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2818

           Summary: Add start and end properties to SeqFeature object
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


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.


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