I Want To Avoid This One Bioperl Warning

Question

[Lee Katz]

Hi all, I am trying to avoid a bioperl warning. I have a mauve alignment that I am parsing and so sometimes there is a sequence with no characters in it. Therefore I get the following warning several times. How can I avoid it?

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

I am trying the following code to try to avoid it, and I think that -verbose=>-1 gives me no change also

return Bio::AlignIO->new(-file=>$outfile,-alphabet=>"dna");

Answer 1

[Neilfws]

I think that you can set verbose on any Bioperl object like this:

my $a = Bio::AlignIO->new(-format => "clustalw");
print "verbose = ", $a->verbose, "\n";
   $a->verbose(-1);
print "verbose = ", $a->verbose, "\n";

# verbose = 0
# verbose = -1

However, I'd advise against hiding warnings; they are generally there for a reason, to tell you something useful. You could always redirect STDERR to a log file if you don't want them printed in the terminal.

[Lee Katz]

Well, I want to address the warning then. How can I force it to recognize that it is a DNA alphabet (but with all gaps)?

[Neilfws]

You have already done that using Bio::AlignIO->new(-alphabet => "dna"). Alphabet is set for the alignment, not for members of the alignment. When you think about it, all gaps = no alphabet. It might be better to remove the all-gaps members first; they are not informative.

[Lee Katz]

Is there a way to not receive this warning and retain gaps...?