[Bioperl-l] concatenating aln splices

Sendu Bala bix at sendu.me.uk
Mon Aug 20 07:43:45 UTC 2007

Joshua Udall wrote:
> Based on several criteria, I've extracted several splices from a
> single alignment and I'm trying to concatenate my selected sequences
> together.  Unfortunately, one of the sequences in the original
> alignment only has gap characters for one or more of the splices.  I'd
> like to keep the gap splices because other downstream aligned bases
> depend on them.
> I don't mind the warnings, in fact I like them, but is there a way to
> stop the splice function from removing the 'gap' sequence from the
> alignment?  Perhaps catching the warning and inserting the gaps
> afterwards might work, but I'm wondering if there's is a simpler
> modification of SimpleAlign.pm that might work.  Any thoughts?

Let us see some code, so we can get a better idea of what you're doing 
and what you've tried.

You can avoid losing sequences during a slice by not doing a slice. 
Instead, remove_columns(). This way you don't have to splice alignments 
together; you go from original alignment to 'spliced' version in one step.

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