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-...@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:
chr11040NM_1234_exon_1
chr25070NM_1234_exon_2
Change the file A to the file B such as:
chr11040NM_1234
chr25070NM_1234
May it is useless in the example. But the way could solve problems I met.
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Jennifer Hillman-Jackson
http://galaxyproject.org
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
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use the Galaxy Development list:
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