Standardising program output
David Martin
damartin at ulrik.uio.no
Sun Sep 10 12:19:34 UTC 2000
To make it easier for script addicts like me, would it be possible to get
som esort of standardised output for certain types of analysis programs
that calculate a single value (or values) for a sequence.
eg
#Name Start End Value1 [Value2 [Value3...]]
This would make automated provessing of large numbers of sequences much
easier. (Yes I know that btwisted doesn't conform to this.)
I looked at infoseq and it looks kind of ugly with all the if
(html) clauses.
Would it not be easier to have a single function
ajFmtPrintData( AjPFile outfile, int outputtype, AjPSeq sequence, AjPList
results);
where the outfile is the file to which to print, outputtype is the type
of text output to produce and is handled by defines so you would use
PLAIN_TEXT, HTML_TEXT, XML_TEXT etc. allowing for more text formats to be
coded without having to touch the application (*), the sequence is used to
get the name, start and
end, and the list contains a list of results that are then printed in a
tab separated manner (probably already converted to strings before adding
to the list.)
There would be a similar function
ajFmtPrintDataHeader( AjPFile outfile, int outputtype , char * appname,
AjPSeq
sequence, AjPList results);
which would print the header line:
#Output from appname at date and time
#Name Start End Val1 Val2 ...
where val1, val2, and so on are teh headers put in an AjList.
It tidies up the coding somewhat and enforces a consistency of output. It
also means that every program can easily be upgraded without recoding when
someone wants a new format.
This could possibly be done better by creating a 'data outfile' object
(-odata output -odformat html or -oresults outfile -orformat plain)
possible output formats could be:
plain (tab delimited columns)
csv (Comma Separated Values)
html
xml (in some format yet to be determined.)
sql (INSERT INTO appnameresults (name, start, end, val1, val2) VALUES
( ... ));
or even some binary formats if people really want to code them.
Thoughts?
..d
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