[Biopython-dev] [Bug 2853] New: Support the "in" keyword with Seq objects / define __contains__ method
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Tue Jun 9 16:02:21 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2853
Summary: Support the "in" keyword with Seq objects / define
__contains__ method
Product: Biopython
Version: Not Applicable
Platform: PC
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
Currently the "in" keyword isn't properly supported in the Seq object, meaning
instead of this:
>>> if "TAG" in my_seq:
>>> print "Found TAG"
you have to do something else like this (using the find method added on Bug
2809):
>>> if my_seq.find("TAG") >= 0 :
>>> print "Found TAG"
In dealing with Bug 2809 we already have a policy in place for dealing with the
alphabet issues, so the code to do this is very simple. Patch to follow.
Because we don't define __contains__ yet, when someone uses "in" at the moment
Python does something indirectly via our __getitem__ method, which means "in"
returns True when used for a single letter (as a string) that is in the
sequence, and False otherwise (e.g. a multi-letter string, or a Seq object).
i.e. currently:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein
>>> my_dna=Seq("AAGTGCTAATAGAAAAA", generic_dna)
>>> "N" in my_dna #works
False
>>> "A" in my_dna #works
True
>>> Seq("A") in my_dna #I think this is broken, should be True
False
>>> "TAG" in my_dna #I think this is broken, should be True
False
>>> "TAG" in my_dna.tostring()
True
>>> "TAG" in str(my_dna)
True
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