Thanks Jen,

Yes, I am working with codingDbSnp files.  The solutions you suggest do the 
work, but they're clunky in requiring a bunch of operations to extract a whole 
codon or to determine whether a particular interval has two or three codons.  
So if someone has a one or two line solution, it would be much appreciated.


On Aug 27, 2012, at 2:04 PM, Jennifer Jackson <> wrote:

> Hi Lee,
> There are a few options .. my guess is you are working with files like 
> snpXXXCodingDbSnp?
> 1 - Using an expression such as this one will extract individual characters 
> from the column, including the commas (treating the column's data like a 
> string)
>  c5.pop(1)
>  = extracts the second character from the column
> 2 - Or, if you want to work with the entire codons, you could use the tool 
> "Convert delimiters to TAB" to fully expand the data. You might want to use 
> other Text Manipulation tools such as "Cut" with this option to get access to 
> specific columns. Or "Condense consecutive characters" if the extra trailing 
> commas in some of these datasets create empty columns (after converting to 
> tabs).
> Hopefully this helps! If there is more feedback from our developers, we'll 
> post more. Others on the list are also welcome to add in comments.
> Best,
> Jen
> Galaxy team
> On 8/27/12 9:44 AM, Jennifer Jackson wrote:
>> Post to mailing list
>> On 8/26/12 11:38 AM, wrote:
>>> Hi Jen,
>>> The ability to use Python commands with the Compute tool seems to be a
>>> very well-hidden gem in Galaxy.  The problem with this nearly
>>> unmentioned gem is the sheer frustration felt when something that
>>> works on the Python command line fails on the Galaxy Compute tool.
>>> What I would like to do is manipulate a column from a UCSC download
>>> that lists two or three codons separated by a comma, e.g.    AAC,GCG,
>>> or  GGT, CAC, TAT,  .   The string-based split command  <
>>> c5.split(",").pop(1) > fails on this data because Galaxy assigned it a
>>> <list> type automatically. All of my attempts to change the data type
>>> to "string" have failed.
>>> Any suggestions?
>>> Lee
> -- 
> Jennifer Jackson

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