XML output format

[Peter Rice]

Graziano P. wrote:
> I am evaluating the possibility to make a parsing of the output of all 
> the EMBOSS algorithms.
> I have found 4 different type of output:
> -sequences in different formats (transeq, seqret, etc);
> -tables (like fuzznuc, iep, etc.)
> -not specific format (like antigenic, remap, etc.)
> -postcript or graphycal output.
> It is very difficult analyzing and extracting information from this type 
> of output. I think that an XML output format for each algorithm would be 
> very useful. NCBI Blast also have an option to convert the output 
> results in XML format. Moreover, there is a "bio-XML" called BSML 
> (Bioinformatic Sequence Markup Language) able to describe bioinformatic 
> sequences.
> Is EMBOSS going to make available in a future release this feature? If 
> no, are there reasons to ignore the power of XML?

If you want XML, then yuo are forcing the results in a specific format, 
so ...

For sequences, you can choose the -osformat.

For reports (tables and 'not specific format' in your list) you can 
choose the -rformat

For graphical output you can choose the graph type

EMBOSS also produces alignments - again, you can choose the -aformat

EMBOSS also produces featout output - you can choose the -offormat and 
this can be the same as some of the available -rformat values

There are programs that produce simple text "outfile" output, but we are 
working on building specific types, with specified formats, for these too.

As for XML - that would be simply an extra output format in each case, 
but which XML format to use ... there are so many to choose from.

Hope this helps,

Peter