Hello Robert,

This tool does sanitize many of the characters required to build this type of regular expression. Some changes to a few of the Text Manipulation tools have been discussed, but nothing is planned for the near term.


For now, the most expedient solution is for you to download the file, edit with a text editor (line command or desktop), then reload.

An updated wrapper that successfully adds parenthesis to the to list of chars changed to tabs with "Convert" might be the simplest change. If you make one, please consider adding it to the Tool Shed and send us an email to galaxy-...@bx.psu.edu to let the development community know about it.

Best wishes,

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#a2664911
“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-columns-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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