[Biopython] CompareAce parser

[Bartek Wilczynski]

Hi Michiel,

I haven't given enough consideration to the maintenance costs of
having parsers like this one in biopython. I think you are right that
it's not  useful in its current state, and I don't think it's worth
putting efforts into improving it. There are already other methods of
motif comparison implemented in bio.Motif and if I was to choose an
external motif comparison software to support in biopython, I would
vote for the STAMP tool from Benos lab. So, in conclusion, I think it
would make sense to deprecate the CompareAce parser.


cheers
Bartek


On Sun, Dec 6, 2009 at 3:31 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> So the reason this parser is so simple and has almost no
>> functionality is just a reflection of the simplicity of
>> the CompareAce files?
>
> Not exactly. CompareAce files can have different outputs, depending on the query given to CompareAce. The simplest query returns only one number. The current CompareAce parser can only parse this output. In other words,
>
>>>> input = open("test.out")
>>>> from Bio.Motif.Parsers import AlignAce
>>>> AlignAce.CompareAceParser().parse(input)
> 0.92130000000000001
>
> is equivalent to
>
>>>> input = open("test.out")
>>>> float(input.read())
> 0.92130000000000001
>
> I am not against having a CompareAce parser in Biopython, but if we have such a parser it should be able to handle more output formats than just the trivial output format.
>
> With this in mind, I think we should either extend the CompareAce parser to handle cases that cannot be trivially handled by a simple Python command, or remove it altogether. If we do keep it in Biopython, there should also be some documentation to cover it, and perhaps a unit test.
>
> --Michiel
>
> --- On Sun, 12/6/09, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
>> From: Peter <biopython at maubp.freeserve.co.uk>
>> Subject: Re: [Biopython] CompareAce parser
>> To: "Bartek Wilczynski" <bartek at rezolwenta.eu.org>
>> Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, biopython at biopython.org
>> Date: Sunday, December 6, 2009, 9:10 AM
>> On Sun, Dec 6, 2009 at 12:58 AM,
>> Bartek Wilczynski
>> <bartek at rezolwenta.eu.org>
>> wrote:
>> > Hi,
>> >
>> > I don't have anything against deprecating, even though
>> I don't the
>> > advantages of doing so. (the module is trivial, but so
>> is the output
>> > of compareACE: a number giving a score between motifs.
>> The score,
>> > however is not trivial and I wouldn't want to
>> reimplement it.)
>> >
>> > cheers
>> >  Bartek
>>
>> So the reason this parser is so simple and has almost no
>> functionality
>> is just a reflection of the simplicity of the CompareAce
>> files? If so, I'd
>> say leave the parser in.
>>
>> Peter
>>
>
>
>
>
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>



-- 
Bartek Wilczynski
==================
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