[BioRuby] the bio-table tool

[Pjotr Prins]

In principle it is streamed.

On Tue, Jul 17, 2012 at 02:09:44PM +0300, George Githinji wrote:
> Hi,
> I have been writing awk scripts to deal with CSV data when i need to.
> Having something in Ruby is totally cool! How good is it at handling
> tables with hundreds of thousands of lines?
> thanks PJ.
> 
> 
> On Tue, Jul 17, 2012 at 1:56 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> > I just want to share the release of one of the most useful tools I
> > have come up with in a while :).
> >
> > Most of us have to deal with tabular data, delivered through
> > spreadsheets, SQL output etc. I found I was repeating myself too
> > often, writing one-off scripts. So I have come up with a command-line
> > tool which allows you to transform and edit(!) tables on the fly,
> > using one-liners.
> >
> > Just now I was wanted to find overlapping marker/geneset combinations
> > in two files. The command was
> >
> >    bio-table --overlap 0,2 NA.SUMMARY.RESULTS.REPORT.1.txt gsea_report_for_1_1342469955711.csv > overlap.1.tab
> >
> > where the columns to compare were 0 and 2. You can diff on columns:
> >
> >   bio-table --diff 0,3 table2.csv table1.csv
> >
> > and merge tables (side by side). You can filter on values
> >
> >   bio-table table1.csv --num-filter "values[3]-values[6] >= 0.05"
> >
> > and regex
> >
> >   bio-table table1.csv --filter "rowname =~ /BGT/ and field[1] =~ /BGT/"
> >
> > and rewrite values
> >
> >   bio-table table1.csv --rewrite 'rowname.upcase!; field[1]=nil if field[2].to_f<0.25'
> >
> > See https://github.com/pjotrp/bioruby-table for more examples.
> >
> > Pj.
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> -- 
> ---------------
> Sincerely
> George
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> Twitter: http://twitter.com/#!/george_l
>