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 <j...@bx.psu.edu>
>To: Robert Curtis Hendrickson <curt...@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: <4e5282c4.3090...@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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>>
>
>--
>Jennifer Jackson
>http://usegalaxy.org
>http://galaxyproject.org/Support
___________________________________________________________
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