[Bioperl-l] Request for advice and pointers on a project to help biologists d o simple formatting and analysis

Amir Karger akarger at CGR.Harvard.edu
Wed Mar 9 13:46:17 EST 2005

In a private mail, Richard Copley wrote:
>Amir Karger wrote:
>> I was thinking it would be useful to have a toolkit of outrageously
>> Perl one-liners.  Here's one:
>>     # Merge two lists, removing duplicates (logical OR)
>>     perl -ne '$seen{$_}++; END {print keys %seen}' file1 file2 > outfile
>sort -u file1 file2

I know that many of the tasks proposed for the Scriptome can be done with
grep, sed, cut, Word, or Excel. I'm planning on implementing head, sort,
join, and lots of others. But how many experimental biologists are familiar
with Unix cut? How many bother to learn even the least fancy Excel
functions?  I think not many, because they have other things to worry about.

One reason so many people have created integrated toolboxes is so that
biologists only need to learn how to use one tool, rather than learning 30
or whatever Unix commands.  The goal of Scriptome is that they only need to
learn one tool AND that the learning curve for that tool is very small. And
we make the learning curve small by using an extremely lightweight interface
(most of solving a problem involves searching on a website) rather than by
trying to create an intuitive GUI.  After all, how many folks  other than
Apple have created GUIs that are intuitive for more than a small subset of


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