[Bioperl-l] concatenating aln splices

Joshua Udall jaudall at gmail.com
Mon Aug 20 14:30:26 EDT 2007


Thanks, Sendu!  That suggestion was exactly what I needed.  I have it worked
out now with the remove_columns function.  Much easier that way :)

Josh

On 8/20/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> 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.
> [snip]
> > 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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