[BioPython] Adding startswith and endswith methods to the Seq object

[Leighton Pritchard]

Howdo,

On 13/04/2009 14:47, "Peter" <peter at maubp.freeserve.co.uk> wrote:

> I'm confident there are many possible use cases for this.
> 
> The example which prompted me to work on this was taking SeqRecord
> objects from sequencing reads (a FASTQ file read in with Bio.SeqIO,
> possible with Biopython 1.50 beta or later) where some include a PCR
> primer associated prefix/suffix which I want to strip off (by slicing
> the SeqRecord).  To do this I need to know if a given SeqRecord's
> sequence starts with (or ends with) a given primer sequence (or a
> tuple of primer sequences).
> 
> e.g. I want to be able to do this:
> 
> primer = "TGACCTGAAAAGAC"
> crop = len(primer)
> #record is a SeqRecord object
> if record.seq.startswith(primer) :
>    record = record[crop:]

[...]
 
> Does this seem like a sensible addition to the Seq object?  It is
> consistent with making the Seq object more like a python string.

Yes it does seem sensible.  I'd quite like to (eventually) have the
capability either to provide ambiguity symbols, or to query with a regular
expression along the lines of re.match() (or maybe the nonexistent
re.endmatch()).  

Since this isn't implemented yet, maybe there's still time to consider this
potential usage in the implementation?

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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