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

Mon Sep 1 07:42:26 UTC 2008

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