[Bioperl-l] Recoding Bio::SimpleAlign
bernd.web at gmail.com
Sat Jul 17 08:21:46 EDT 2010
Thanks for your work on this.
Just a few remarks.
-is changing methods names indeed needed? this will break existing
code (for some time)
-i am not sure how naming is generally done now in BioPerl, but is
used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has
an "_" followed by a capital. I'd stick with each_seq like names. You
now changed it too "each_Seq" but gap_char for example remained
gap_char. But surely others know better how/if to change naming.
> 2. gap chars/missing chars are more consistent in the package
> Default values for gap char and missing char are now set in the package.
> Calling/Setting gap char should be made by calling $aln->gap_char("-").
So the change here is that now the default values are actually set in
new, instead of setting a the default by calling gap_char.
> Another example, the method is renamed to give a clearer information.
> $aln->purge is renamed into $aln->remove_redundant_Seqs
Purge to me is a clear name in aln context ;-)
> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps
But there was already a remove_gaps method.
$aln2 = $aln->remove_gaps
Function : Creates an aligment with gaps removed
Title : splice_by_seq_pos
Usage : $status = splice_by_seq_pos(1);
Function: splices all aligned sequences where the specified sequence
So remove_gaps now takes an optional argument to indicate a
'reference' sequence for splicing?
More information about the Bioperl-l