Dreaming about bio-spreadsheet
One of the often occuring task in my work is to present results of an analysis in some kind of table. I have used for such purpose quite a number of approaches, starting from generating simple HTML file, through fetching of SQL data into table stored in a wiki, up to using Rails. One of the dreams I have recently is a web-based spreadsheet that would allow me to apply some specific piece of code over every row/column and show resulting table.
A simple mockup is shown above. In this example, a code:
print " <img src="http://www.pdb.org/pdb/images/#{column_1}_bio_r_250.jpg>"
… iterated over first column containing PDB codes, would substitute these codes with an image of a protein from PDB server.
In other words I dream about simple (single file would be the best – I like the approach Sinatra framework is taking) web-based programmable spreadsheet. Something like Resolver One, but simpler. Is there anything like that available?
So data is in rows and columns are “transformations”. Why do you think this is superior to a flow-chart with vector(i.e. rows) input?
I am not sure is this fits the bill…but some folks at the EBI have created a java-based platform for data storage and annotation. It is called ISAcreator and can be found here:
http://isatab.sourceforge.net/isacreator.html
Burke
It seems like you could probably throw something together with dabbleDB that would fit the bill…
I’m mostly stuck with Python doing this kind of things. Each time I just copy over the older script, change the number of items parsed from a single line of data file, and then change print statements
That’s fairly easy, but I guess this could be extended to a more-or-less universal script, counting columns on its own, and accepting string parameters with $1, $2 … embedded to denote column contents.
Also, there’s awk (gawk), which I guess could do the job best, but my knowledge of gawk is limited to simple column extraction, like
gawk '{print $2"\t"$5}' datafile.tsvoops, missed a closing ‘ after right curly brace above
Thank you all for the comments.
Marcin, it’s all about presentation to the non-programming colleagues and looking for possibility to avoid Excel files
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Burke, thanks a lot, I wasn’t aware of ISAcreator. Need to have a look.
Tyler, duh!, DableDB
I’ve used it so long ago I forgot about its existence.
Bogdan, I have a similar workflow (but use Perl one-liners instead of gawk) however as I pointed to Marcin, it’s the “presentation” part that dictates other requirements
. I’ve corrected your gawk snippet.