[Bioperl-l] issues with Bio::SimpleAlign add_seq function
cjfields at illinois.edu
Thu Mar 19 19:04:24 EDT 2009
I forget, but was this committed to svn? Did it pass tests?
I don't think it was incorporated into 1.6 ...
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
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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