Hi Curtis, To accomplish things like your "split" command I have had success with Compute using c1.split('(').pop(0) HTH - Russell

Message: 1 Date: Mon, 22 Aug 2011 09:24:36 -0700 From: Jennifer Jackson <jen@bx.psu.edu> To: Robert Curtis Hendrickson <curtish@uab.edu> Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] Text Manipulation > Compute > c1[1:c1.find("(")] fails Message-ID: <4E5282C4.3090703@bx.psu.edu> Content-Type: text/plain; charset=windows-1252; format=flowed

Hello Curtis,

There is some more feedback from our developers. In your own instance, this is the recommended change:

Edit ->

tools/stats/column_maker.py

To add ->

__ob__ and __cb__ to the mapped_str dict.

Perhaps this will help if you still needed work-around (or others reading this thread).

Best!

Jen Galaxy team

...

On 7/20/11 1:13 PM, Robert Curtis Hendrickson wrote:

...

Folks,

I have a column c1 that has entries like ?GXP_297346(PVALB/human)?.

I?m trying to use Text Manipulation > Compute to strip off the ?(?)? portion, leaving only the accession (which can vary in length).

I have tried a variety of things that work in my python command line, but fail here, for example:

c1[1:c1.find("(")]

or

c1.split('(')[0]

This gets mangled:

An error occurred running this job: Expression "c1__ob__1:c1.find("(")__cb__" likely invalid.

Or

An error occurred running this job: Expression "c1.split("(")__ob__0__cb__" likely invalid.

Please help. This is driving me crazy.

Searching the list, I find only

http://gmod.827538.n3.nabble.com/inputs-sanitization-tt2664336.html#a266 4911

?Inputs sanitization? which seems to indicate this is a global mapper that can only be disabled with dire security consequences.

And

http://gmod.827538.n3.nabble.com/substring-sequence-on-coordinate-in-col umns-tt3026255.html#a3048100

?substring sequence on coordinate in columns? which doesn?t ever answer the question about how to get compute to work.

Thanks,

Curtis

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