[Bioperl-l] concatenating aln splices
jaudall at gmail.com
Mon Aug 20 18:30:26 UTC 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 :)
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.
> > 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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