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

Mark A. Jensen maj at fortinbras.us
Thu Mar 19 19:48:15 EDT 2009


Done (#2793), and accepted by moi-
MAJ
----- 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 7:18 PM
Subject: Re: [Bioperl-l] issues with Bio::SimpleAlign add_seq function


> ok, that's what I thought.
>
> As for (1), if there is a discrepancy btwn how methods are using  indices then 
> this is a bug (odd that it didn't pop up before).  Could  someone file this in 
> bugzilla?
>
> chris
>
> On Mar 19, 2009, at 5:08 PM, Mark A. Jensen wrote:
>
>> Hang on, looks like that change made it into the trunk: issue 2 is  resolved 
>> in the HEAD revision
>> of Bio::SimpleAlign 
>> (http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/SimpleAlign.pm 
>>  ).
>> (revision 15533/cjfields)...
>> ----- 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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