XML output format

Peter Rice pmr at ebi.ac.uk
Tue Jul 1 16:18:30 UTC 2003


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




More information about the EMBOSS mailing list