[Bioperl-l] TCofee does not accept named arguments and issue with output option

[Carnë Draug]

Hi

the TCoffee module does not options of the named argument type:

-arg => option

one needs to do like

'arg' => option

Is there a special reason for this? I tracked down this to the commit

7b2f9189fe2af4f99f1c3d7fe79c732bfe01261e

12 years ago[1]. A comment on the code actually says "don't want named
parameters"[2] (though the commit message sounds pretty innocuous
"migrated to new Bio::Root::RootI chained new"). Is there a reason for
this? The rest of bioperl has no issue with named parameters, and the
API should be the same as Clustalw which also has no problem with it.
This is very easy to fix, I can submit a pull request no problem.

Also, shouldn't the code complain in the case of non-supported
options? Took me a very long time to find out the problem because
there was no complaints coming from the code.

There is also a problem with the way it handles the output option.
I'll have to look closer into it, but the documentation is simply
incorrect. "'output' => 'fasta_aln'" gives an error while just 'fasta'
(undocumented), works fine.

Carnë
[1] https://github.com/carandraug/bioperl-run/commit/7b2f9189fe2af4f99f1c3d7fe79c732bfe01261e
[2] https://github.com/carandraug/bioperl-run/commit/7b2f9189fe2af4f99f1c3d7fe79c732bfe01261e#L0R374