[BioPython] regular expression and filtering dna strings

[Leighton Pritchard]

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Hi Enrico,

If your DNA strings never contain anything other than ACGT, then a
result other than 'None' for re.search('[^ACGT]', your_string) will be
diagnostic for non-DNA sequences.  A None result will not, however, be
diagnostic for DNA...

Python 2.3.2 (#1, Dec 12 2003, 11:27:04)
[GCC 3.3.2 20031022 (Red Hat Linux 3.3.2-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
|>> import re
|>> a = 'ACGTGTACGT'
|>> b = 'ACAGFTAGAT'
|>> re.search('[^ACGT]', a)
|>> print re.search('[^ACGT]', a)
None
|>> print re.search('[^ACGT]', b)
<_sre.SRE_Match object at 0xbf511368>

HTH,

enrico curiotto wrote:
| Hello everybody,
| I have the following problem:
| A have a series of strings, some of them are DNA strings (so they
| contain only ACGT), other not.
| How can I filter out not DNA strings?
| Maybe this can be properly done quickly with regular expression
| in python, without using biopython.
| Does anyone know how to do that with regular expression ?
| Thank you very much,
| Enrico.
|
|
|
|
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- --
Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc at scri.sari.ac.uk
W: http://bioinf.scri.sari.ac.uk/lp/index.shtml
T: +44 (0)1382 562731 ext.2405		F: +44 (0)1382 568578
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