[BioPython] How to automate "save column scores to file" in clustalx?

[Peter]

On Fri, Feb 6, 2009 at 3:52 AM, Hyunchul Kim <hyunchul.mailing at gmail.com> wrote:
> Hi, all
>
> I need 'quality scores' of clustal.
> ClustalW provides only 4 degrees by simbols (*, :, ., ' ') and biopython
> supports it.
> ClustalX provides quality scores and it can be saved via menu 'Quality' ->
> 'save column scores to file'.
> However, I couldn't figure out how to do it automatically such as command
> line or biopython scripting.
>
> More specifically,
> ClustalW can produce the 'quality scores'?

Not that I am aware of.  You could try looking at the source code or
email the authors.

> or ClustalX can produce output containing 'quality scores' by command line?

Not that I am aware of.  You could try looking at the source code or
email the authors.

> or Any other suggestions?

Do you know how this score is calculated?  Perhaps it can be
calculated from the alignment columns themselves?  Certainly the four
symbols can be calculated from the column composition ("*" for 100%
conserved, ":" if there are all in the same amino acid strong group,
"." if they are all in the same amino acid week group, space
otherwise).

Peter