[Bioperl-l] Retaining seqnos from clustal output in AlignIO

[Dave Messina]

Hi Lee,

I thought there was a way to do this, but looks like we have an option to
AlignIO->new() to do the opposite:

-displayname_flat => 1 [optional]
                                to force the displayname to not show
start/end
                                information

Since the syntax

id/start-end

is special, and I believe actually rewritten depending on how the sequence
or alignment is manipulated, you might try keeping your strand and
coordinate metadata separate from the id — for example, in the description
field (hacky though it may be).

Sequences like these are LocatableSeqs in BioPerl. Here are details:
http://doc.bioperl.org/bioperl-live/Bio/LocatableSeq.html


Dave





On Mon, Apr 18, 2011 at 17:25, Lee Katz <lskatz at gmail.com> wrote:

> Hi, I have a large Clustal alignment but I want to sort the sequences and
> retain the coordinate numbers on the sides.  I've also hacked in strand
> information into the sequence name, but that's another story.
>
> How can I use an "in" alignio and an "out" alignio and still retain the
> coordinate numbers?  I can't find an option to keep them.  Thanks.
>
> SeqYYY.fna/1/232361-241520
> TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50
> SeqZZZ.fna/1/233928-243087
> TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50
> AnotherSeq.fna/1/1-10089
> TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50
>
> --
> Lee Katz
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