Well, having similarly basic tools (in Galaxy) that can be performed on the commandline, such as "sort" or "cut" I just wondered how come a "uniq" is not there on the tool panel in some form/name.

Thanks for the feedback Rory !

On 2011-05-06 15:56, Rory Kirchner wrote:

Is there a reason why just using the command line tool isn't workable for you? Personally, I'm happy when I can just do something quick like that.

Also you can simplify your command with sort filename | uniq.

-rory

On May 6, 2011, at 9:45 AM, Roman Valls wrote:

...

Hey galaxy users,

Thats a fairly good question from one of my colleagues. I've looked through the menus (mainly "Text Manipulation" and "Filter and Sort"(Select)), googled (on the mailing list archives too), but couldn't find an answer: How should I remove duplicates on plain text files without resorting to:

"echo file|sort|uniq" before uploading the file/text.

or

Putting a regexp together to replace the duplicate occurences as in:

http://www.regular-expressions.info/duplicatelines.html

I'm pretty sure I'm missing some really basic stuff here... is this basic operation something supposed to be done outside galaxy perhaps ?

Thanks in advance !

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Hi Peter and Roman,

The "Count" tool under "Statistics" section provides uniq-like functionality. If you run this tool by selecting all columns under "Count occurrences of values in column(s)" field, your output will contain one line per record, with the 1st column containing the number of occurrences of each record.

Hope this answers your question. Thanks for using Galaxy, Guru.

On Fri, May 6, 2011 at 10:22 AM, Peter Cock p.j.a.cock@googlemail.comwrote:

On Fri, May 6, 2011 at 3:16 PM, Roman Valls brainstorm@nopcode.org wrote:

...

Well, having similarly basic tools (in Galaxy) that can be performed on the commandline, such as "sort" or "cut" I just wondered how come a "uniq" is not there on the tool panel in some form/name.

Thanks for the feedback Rory !

That's a timely question - I was also looking for something within Galaxy to take a text file and remove duplicate lines.

Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of 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 local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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