Hi Jen,

Thank you for your help. The Galaxy tools can do many things!

Sent: Friday, August 30, 2013 8:31 AM

To: 师云

Subject: Re: [galaxy-user] Question about expression in Galaxy tools

Hello,

There are some tools in the group 'Text Manipulation' that do this sort of manipulation directly. Combined, many basic "unix" functions can be performed. Combine them to create custom tools using Workflows - even place them in your tool menu for seamless access.

To move from file A to file B, use tools such as these as a rough example:
* Convert delimiters to TAB (convert all "_" to tabs)
* Add column to an existing dataset (could include a single "_" char, to be merged later)
* Cut columns from a table (can be used to rearrange and leave behind unwanted columns)
* Merge Columns together (merge the new "_" back where you want it)

Compute and Select have some character filters on them for security reasons. If you were running your own Galaxy and it wasn't public, these could be removed of course. Also, a tool from the Tool Shed such as the 'Tool factory' could be used to turn pretty much any custom unix/shell (or other!) script that acts on text data into a full fledged, single tool - the tool that creates tools! That new tool could even be for a publicly hosted server use if you wanted to do that (I'd recommend a security test first though, as with any new tool!). And don't leave Tool Factory active on a public server - bad things could happen.

I am positive others have come up with many more solutions in all sorts of flavors. Discussions like this are good for the galaxy-dev@bx.psu.edu mailing list if you are interested in interacting with the development community. More about the list is here, about joining, posting, and following along:
http://wiki.galaxyproject.org/Support#Mailing_Lists

Thanks!
Jen
Galaxy team

On 8/29/13 9:38 AM, 师云 wrote:

Hello everyone,

I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was possible like this?

The file A:

chr1    10    40    NM_1234_exon_1

chr2    50    70    NM_1234_exon_2

Change the file A to the file B such as:

chr1    10    40    NM_1234

chr2    50    70    NM_1234

May it is useless in the example. But the way could solve problems I met.
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Jennifer Hillman-Jackson
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