[Bioperl-l] Bio::Tools::dpAlign feature request

Chris Fields cjfields at illinois.edu
Mon Sep 1 17:49:56 UTC 2008 

On pSW: I agree, I don't think it is worth maintaining it considering  
there are actively supported C/C++-based toolkits with similar  
functionality (SeqAn) and Petr's BioLib initiative will likely be a  
more maintainable effort.

chris

On Sep 1, 2008, at 2:42 AM, Jason Stajich wrote:

> Safe to ignore the tests.  Those that are failing aren't even test  
> for Bio::Align::dpAlign - but were written to test a bug that has  
> not been fixed in the EVD module if I remember correctly that is why  
> they are marked in a TODO block, but I can't tell if the Test.pm is  
> actually skipping these tests or not.
>
> I think we probably need to deprecate some of these modules as there  
> is no maintainer of Ewan's code in here.
>
> At a minimum we need to modularlize the tests for these modules into  
> separate t dir and fix the need for multiple Makefile.PL in here and  
> probably move to Build.PL
>
> -jason
> On Aug 28, 2008, at 11:00 AM, Yee Man Chan wrote:
>
>>
>> Hi Alexie
>>
>> My understanding is that you can ignore these failures.
>>
>> I believe test cases 17-20 were added by Jason Stajich before I  
>> added the feature you requested. I am not sure what he was doing  
>> there.
>>
>> I suppose he can give you the definite answer to whether this is  
>> something important or not.
>>
>> By the way, did you try out the new feature? Does it work?
>>
>> Thanks
>> Yee Man
>>
>> --- On Thu, 8/28/08, Alexie Papanicolaou <apapanicolaou at ice.mpg.de>  
>> wrote:
>>
>>> From: Alexie Papanicolaou <apapanicolaou at ice.mpg.de>
>>> Subject: Re: Bio::Tools::dpAlign feature request
>>> To: "Yee Man Chan" <ymc at yahoo.com>
>>> Date: Thursday, August 28, 2008, 6:15 AM
>>> hi
>>>
>>> is the version you emailed me newer or older than the
>>> subversion one?
>>>
>>> i'm testing the subversion version for bioperl-ext and
>>>
>>> not ok 17 # TODO evalues vary based on platform, needs
>>> fixing
>>> #   Failed (TODO) test at test.pl line 156.
>>> #          got: '2027805538'
>>> #     expected: '1764904'
>>> not ok 18 # TODO evalues vary based on platform, needs
>>> fixing
>>> #   Failed (TODO) test at test.pl line 157.
>>> #          got: '-1375488148'
>>> #     expected: '1764872'
>>> not ok 19 # TODO evalues vary based on platform, needs
>>> fixing
>>> #   Failed (TODO) test at test.pl line 158.
>>> #          got: '-808808307'
>>> #     expected: '1764872'
>>> not ok 20 # TODO evalues vary based on platform, needs
>>> fixing
>>> #   Failed (TODO) test at test.pl line 159.
>>> #          got: '-2118162890'
>>> #     expected: '1764872'
>>>
>>> you think these are ok to ignore?
>>>
>>>
>>> On Fri, 2008-08-01 at 21:03 -0700, Yee Man Chan wrote:
>>>
>>>> Hi Alexie
>>>>
>>>>  Attached are the files that contains the feature
>>> you requested. linspc.c is the one that does the work and
>>> test.pl has a test case for it. The scoring scheme is as
>>> described before. Please let me know if it works.
>>>>
>>>> Yee Man
>>>>
>>>> --- On Wed, 7/30/08, Alexie Papanicolaou
>>> <apapanicolaou at ice.mpg.de> wrote:
>>>>
>>>>> From: Alexie Papanicolaou
>>> <apapanicolaou at ice.mpg.de>
>>>>> Subject: Re: Bio::Tools::dpAlign feature request
>>>>> To: ymc at yahoo.com
>>>>> Date: Wednesday, July 30, 2008, 2:44 PM
>>>>> Oh sorry
>>>>>
>>>>> Say match=3 and mismatch=-1, gopen= -10, gext=-5
>>>>> for aligning
>>>>> seq1: ATG
>>>>> seq2: ATT
>>>>> match: 3,3,-1
>>>>>
>>>>> seq1: AT-G
>>>>> seq2: ATTG
>>>>> match: 3,3,-1,-10,3
>>>>>
>>>>> is that possible? or am I missing something? I
>>> was only
>>>>> today wondering
>>>>> if it is even possible...
>>>>>
>>>>> a
>>>>>
>>>>>
>>>>> Yee Man Chan wrote:
>>>>>> Sorry, I don't quite get it. Can you
>>> give me an
>>>>> example of the output you want?
>>>>>>
>>>>>> Yee Man
>>>>>>
>>>>>> --- On Wed, 7/30/08, Alexie Papanicolaou
>>>>> <apapanicolaou at ice.mpg.de> wrote:
>>>>>>
>>>>>>
>>>>>>> From: Alexie Papanicolaou
>>>>> <apapanicolaou at ice.mpg.de>
>>>>>>> Subject: Re: Bio::Tools::dpAlign feature
>>> request
>>>>>>> To: ymc at yahoo.com
>>>>>>> Date: Wednesday, July 30, 2008, 9:50 AM
>>>>>>> Dear Yee Man,
>>>>>>>
>>>>>>> Do you think it is possible to code a
>>> method for
>>>>> creating a
>>>>>>> delimited
>>>>>>> (space or comma) "score-line"?
>>>>>>>
>>>>>>> I'd like to parse it into an array
>>> and have
>>>>> the
>>>>>>> individual score for
>>>>>>> each alignment position. Is it easy to
>>> do?
>>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>> Yee Man Chan wrote:
>>>>>>>
>>>>>>>> Hi Alexie
>>>>>>>>
>>>>>>>>  How about I implement the simple
>>> case?
>>>>>>>>
>>>>>>>> So for match = +3, mismatch = -1,
>>>>>>>>
>>>>>>>> A and R = +3
>>>>>>>> A and Y = -1
>>>>>>>> A and B = -1
>>>>>>>> A and D = +3
>>>>>>>> A and N = +3
>>>>>>>> A and X = -1
>>>>>>>>
>>>>>>>> What do you think?
>>>>>>>> Yee Man
>>>>>>>>
>>>>>>>>
>>>>>>>> --- On Tue, 7/29/08, Alexie
>>> Papanicolaou
>>>>>>>>
>>>>>>> <apapanicolaou at ice.mpg.de> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> From: Alexie Papanicolaou
>>>>>>>>>
>>>>>>> <apapanicolaou at ice.mpg.de>
>>>>>>>
>>>>>>>>> Subject: Re: Bio::Tools::dpAlign
>>> feature
>>>>> request
>>>>>>>>> To: ymc at yahoo.com
>>>>>>>>> Date: Tuesday, July 29, 2008,
>>> 10:58 AM
>>>>>>>>> Dear Yee Man,
>>>>>>>>> hello, I was wondering how is
>>> this
>>>>> progressing and
>>>>>>>>>
>>>>>>> if you
>>>>>>>
>>>>>>>>> need help?
>>>>>>>>>
>>>>>>>>> many thanks
>>>>>>>>> alexie
>>>>>>>>>
>>>>>>>>> Yee Man Chan wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi Alexie
>>>>>>>>>>
>>>>>>>>>>  There are two ways to
>>> compute the
>>>>> score for
>>>>>>>>>>
>>>>>>> each
>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> aligned basepair in dpAlign
>>> module. One is
>>>>>>>>>
>>>>>>> match/mismatch
>>>>>>>
>>>>>>>>> if you specify your sequence as
>>> DNA and
>>>>> the other
>>>>>>>>>
>>>>>>> is a
>>>>>>>
>>>>>>>>> scoring matrix if you specify
>>> your
>>>>> sequence as
>>>>>>>>>
>>>>>>> protein.
>>>>>>>
>>>>>>>>> Obviously, the latter can
>>> completely
>>>>> dominate the
>>>>>>>>>
>>>>>>> former.
>>>>>>>
>>>>>>>>> If you take the time to type the
>>> scoring
>>>>> matrix
>>>>>>>>>
>>>>>>> file, then
>>>>>>>
>>>>>>>>> you can handle those IUPAC code
>>> by
>>>>> specifying the
>>>>>>>>>
>>>>>>> sequence
>>>>>>>
>>>>>>>>> as proteins.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>  If you think this is too
>>>>> troublesome, then
>>>>>>>>>>
>>>>>>> I might
>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> be able to extend the
>>> match/mismatch route
>>>>> to
>>>>>>>>>
>>>>>>> handle IUPAC
>>>>>>>
>>>>>>>>> codes. But the problem here is,
>>> how should
>>>>> I score
>>>>>>>>>
>>>>>>> a match
>>>>>>>
>>>>>>>>> of A and W when match is +3 and
>>> mismatch
>>>>> is -1?
>>>>>>>>>
>>>>>>> Should it
>>>>>>>
>>>>>>>>> have a score of +3/3 = +1 for
>>> match or
>>>>> +3/3-1*2/3
>>>>>>>>>
>>>>>>> = +1/3?
>>>>>>>
>>>>>>>>> Do you know what the convention
>>> is? If
>>>>> not, maybe
>>>>>>>>>
>>>>>>> you can
>>>>>>>
>>>>>>>>> tell me what you think the score
>>> will be?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Yee Man
>>>>>>>>>>
>>>>>>>>>> --- On Thu, 6/26/08, Alexie
>>>>> Papanicolaou
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> <apapanicolaou at ice.mpg.de>
>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> From: Alexie
>>> Papanicolaou
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> <apapanicolaou at ice.mpg.de>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> Subject:
>>> Bio::Tools::dpAlign
>>>>> feature
>>>>>>>>>>>
>>>>>>> request
>>>>>>>
>>>>>>>>>>> To: ymc at yahoo.com
>>>>>>>>>>> Date: Thursday, June 26,
>>> 2008,
>>>>> 4:15 AM
>>>>>>>>>>> Dear Yee Man Chan,
>>>>>>>>>>>
>>>>>>>>>>> Many thank you for this
>>> module. I
>>>>> like it
>>>>>>>>>>>
>>>>>>> very
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> much. I was
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> wondering if
>>>>>>>>>>> it would be possible for
>>> you to
>>>>> allow for
>>>>>>>>>>>
>>>>>>> IUPAC
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> DNA codes.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> I see it is in your TODO
>>> list and
>>>>> I hoped
>>>>>>>>>>>
>>>>>>> to
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> inspire you
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> :-)
>>>>>>>>>>>
>>>>>>>>>>> Even a simple measure
>>> with the
>>>>> degenerate
>>>>>>>>>>>
>>>>>>> base
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> containing
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> the aligned
>>>>>>>>>>> base count as a
>>> (perfect) match
>>>>> would be
>>>>>>>>>>>
>>>>>>> very
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> useful to me
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> (i'm sorry, i
>>>>>>>>>>> 'm not a good coder
>>> to do it
>>>>> myself).
>>>>>>>>>>>
>>>>>>>>>>> many thanks for your
>>> work so far.
>>>>>>>>>>> alexie
>>>>>>>>>>>
>>>>>>>>>>> -- 
>>>>>>>>>>> --
>>>>>>>>>>> "Eppur si
>>> evolve"
>>>>> ("And yet
>>>>>>>>>>>
>>>>>>> it
>>>>>>>
>>>>>>>>>>> evolves")
>>>>>>>>>>> -Galileo Jr (ca 21st
>>> century)
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Alexie Papanicolaou
>>>>>>>>>>> Entomology
>>>>>>>>>>> Max Planck Institute for
>>> Chemical
>>>>> Ecology
>>>>>>>>>>> Hans Knoell Str 8
>>>>>>>>>>> Jena 07745
>>>>>>>>>>> Germany
>>>>>>>>>>> Email
>>> apapanicolaou at ice.mpg.de
>>>>>>>>>>> Tel +493641571561
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> -- 
>>>>>>>>> --
>>>>>>>>> "Eppur si evolve"
>>> ("And yet
>>>>> it
>>>>>>>>> evolves")
>>>>>>>>> -Galileo Jr (ca 21st century)
>>>>>>>>>
>>>>>>>>> "One Galileo in two
>>> thousand years is
>>>>>>>>>
>>>>>>> enough."
>>>>>>>
>>>>>>>>> -Pope Pius XII
>>>>>>>>> --
>>>>>>>>> Alexie Papanicolaou
>>>>>>>>> Entomology
>>>>>>>>> Max Planck Institute for
>>> Chemical Ecology
>>>>>>>>> Hans Knoell Str 8
>>>>>>>>> Jena 07745
>>>>>>>>> Germany
>>>>>>>>> Email apapanicolaou at ice.mpg.de
>>>>>>>>> Tel +493641571561
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> -- 
>>>>>>> --
>>>>>>> "Eppur si evolve" ("And
>>> yet it
>>>>>>> evolves")
>>>>>>> -Galileo Jr (ca 21st century)
>>>>>>>
>>>>>>> "One Galileo in two thousand years
>>> is
>>>>> enough."
>>>>>>> -Pope Pius XII
>>>>>>> --
>>>>>>> Alexie Papanicolaou
>>>>>>> Entomology
>>>>>>> Max Planck Institute for Chemical
>>> Ecology
>>>>>>> Hans Knoell Str 8
>>>>>>> Jena 07745
>>>>>>> Germany
>>>>>>> Email apapanicolaou at ice.mpg.de
>>>>>>> Tel +493641571561
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> -- 
>>>>> --
>>>>> "Eppur si evolve" ("And yet it
>>>>> evolves")
>>>>> -Galileo Jr (ca 21st century)
>>>>>
>>>>> "One Galileo in two thousand years is
>>> enough."
>>>>> -Pope Pius XII
>>>>> --
>>>>> Alexie Papanicolaou
>>>>> Entomology
>>>>> Max Planck Institute for Chemical Ecology
>>>>> Hans Knoell Str 8
>>>>> Jena 07745
>>>>> Germany
>>>>> Email apapanicolaou at ice.mpg.de
>>>>> Tel +493641571561
>>>>
>>>>
>>>>
>>>
>>> -- 
>>> -- 
>>> "Eppur si evolve" ("And yet it
>>> evolves")
>>> -Galileo Jr (ca 21st century)
>>>
>>> "One Galileo in two thousand years is enough."
>>> -Pope Pius XII
>>> -- 
>>> Alexie Papanicolaou
>>> Entomology
>>> Max Planck Institute for Chemical Ecology
>>> Hans Knoell Str 8
>>> Jena 07745
>>> Germany
>>> Email apapanicolaou at ice.mpg.de
>>> Tel +493641571561
>>
>>
>>
>
> Jason Stajich
> jason at bioperl.org
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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