New report format needed?

Peter Rice pmr at
Wed Mar 10 09:11:12 UTC 2004

Henrikki Almusa wrote:

> There are few programs in Emboss package that create a report on sequence and 
> its "statistics". For example are pepstat, cai, cusp and geecee. Now each of 
> these have nearly similar formats, but not same. Basicly it would be good, if 
> these were same and also have the header and tail sections as report format 
> has.
> Format could be simple. Either rows like this 
> # [Calculated type]: [value]
> or
> 			ValueType1	ValueType2	ValueType3 ...
> ListType1
> ListType2
> ListType3

Yes ... I plan to add this very soon. The plan is like this:

Add a new output ACD type "outdata"

Replace "outfile" with "outdata" and define (as for report) the values

Provide several output formats (includnig some kind of XML) but default 
to text close to the original output

A complication: some programs produce several outputs like this in one 
text file. For these, I plan to define "outdata" once for each section, 
with a default of appending to the original outdata file - but the 
possibility to write to another file is you want to save each section 

> Also I wondered if it would a good idea to combine some of these programs? 
> Since some of these calculate only one value.

We can investigate that. I feel that this will mean multiple outdata 
definitions and may be more confusing in most cases.

Thanks for the suggestion


More information about the emboss-dev mailing list