[Bioperl-l] issues with Bio::SimpleAlign add_seq function

Mark A. Jensen maj at fortinbras.us
Thu Mar 19 19:10:09 EDT 2009


This is in the head revision of the trunk; happened post 1.6. I think the issue 
scrolled off
my screen before I confirmed all tests. Looks like it was a cjfields commit; did 
tests go through
for you?
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "albezg" <albezg at gmail.com>; <bioperl-l at bioperl.org>
Sent: Thursday, March 19, 2009 7:04 PM
Subject: Re: [Bioperl-l] issues with Bio::SimpleAlign add_seq function


>I forget, but was this committed to svn?  Did it pass tests?
>
> I don't think it was incorporated into 1.6 ...
>
> chris
>
> On Mar 19, 2009, at 5:00 PM, Mark A. Jensen wrote:
>
>> Alexandr- I did write a patch for issue 2); I can make it available  to you. 
>> It does
>> a proper insertion of a new seq at the specified $order, pushing the  rest 
>> down
>> to make room. Not sure if the Core would like this committed?
>> cheers Mark
>> ----- Original Message ----- From: "albezg" <albezg at gmail.com>
>> To: <bioperl-l at bioperl.org>
>> Sent: Thursday, March 19, 2009 5:30 PM
>> Subject: [Bioperl-l] issues with Bio::SimpleAlign add_seq function
>>
>>
>>> Hi all,
>>> I'm using bioperl-1.6. Here are some things that bother me about
>>> Bio::SimpleAlign add_seq function
>>>
>>> 1) Sequence order is counted from 0 not 1, unlike in other functions,
>>> such as get_seq_by_pos and select.
>>> 2) If position $order is already occupied then the old sequence is
>>> removed. Is there a way to insert a new sequence in the middle of an
>>> alignment?
>>>
>>> Alexandr
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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>
>
> 



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