[Bioperl-l] Writing bp_grep
Fields, Christopher J
cjfields at illinois.edu
Sun May 13 17:54:09 UTC 2012
Bio::Tools::SeqPattern could be used (and improved upon if needed) for pattern generation.
chris
On May 13, 2012, at 12:36 PM, Hilmar Lapp wrote:
> And of course there's tacg (though I have never used it - not sure about its status):
>
> Mangalam HJ (2002) tacg – a grep for DNA. BMC Bioinformatics 3:8
> doi:10.1186/1471-2105-3-8
>
> -hilmar
>
> On May 13, 2012, at 1:26 PM, Peter Cock wrote:
>
>> On Sunday, May 13, 2012, Carnë Draug wrote:
>>
>>> Hi everyone
>>>
>>> I'm starting to write a grep tool for sequences (bp_grep). The idea is
>>> to have something just like grep but for DNA and protein sequences
>>> with most of the options that make sense in this context (print the
>>> filename or sequence name only, position, without match search, count,
>>> etc). I was wondering if anyone has any piece of code that could fit
>>> in it or started something similar but just never finished.
>>>
>>> Thanks,
>>> Carnë
>>>
>>
>> This sounds like EMBOSS preg,
>> http://emboss.open-bio.org/wiki/Appdoc:Preg
>>
>> I thought they had a nucleotide equivalent but I can't see
>> it right now....
>>
>> Peter
>>
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>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
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