Thanks! This worked perfectly. 
luce

On 9 Dec, 2011, at 2:31 PM, Dave Clements wrote:

> Hi Luce,
> 
> I'm forwarding this question to the Galaxy-User mailing list, as I think this 
> is a pretty common situation.
> 
> Here's how I replace text in a column.  It's a two step process for each 
> dataset.
> 
> First go to Text Manipulation -> Compute.
> 
> In the Add expression text box enter
> 
>   columnNum.replace("oldVal", "newVal")
> 
> In your case I think this is
> 
>   c4.replace("MACS_peak_", "treatment1_peak_", 1)
> 
> "replace" is a Python character string operation, and c4 is the character 
> string column we are working on.  I added the 1 out of paranoia.  This tells 
> galaxy to only replace the first occurrence of the old string, in each line.  
> Care must be taken to avoid more replacement than you want.
> 
> Executing this will create a dataset with a new column at the end.
> 
> Now, use the Text Manipulation -> Cut operation to substitute the new column 
> in place of the old column.
> 
> Does that do the trick?
> 
> Thanks,
> 
> Dave C.
> 
> On Thu, Dec 8, 2011 at 4:24 PM, las2017 <las2...@med.cornell.edu> wrote:
> I have two ChIPSeq datasets, and I am trying to find the common and distinct 
> peaks between them and visualize them. I end up with a MACS bed file for each 
> (listing a bunch of MACS_peaks). I then use the Intersect and Subtract tools 
> from the Genomic Intervals tab and end up with the peaks I want. However, 
> because of the way that MACS names its peaks, there can end up being some 
> peaks named the same way in both files (because, for example, peak 20 in 
> file1 is from position 300,000-300,500 but peak 20 in file 2 is from position 
> 320,000-320,500). So, I can end up with multiple peaks with the same name. 
> Because all the peak names have the same form, it can also be difficult to 
> tell them apart when visualizing them in the UCSC Genome Browser.
> 
> What I would like to do is to be able to edit the bed file to change the text 
> MACS_peak_<number> to, say, treatment1_peak_<number> so that peak 20 would 
> now still be numbered 20 in both files, but would have a different label. 
> This would be pretty easy to do using regular expressions and sed.
> 
> I know there have been a few posts about text manipulation, and I know that 
> there is a text manipulation tab, but I can't seem to find an easy way to do 
> what I want to do.
> 
> Any advice?
> 
> Thanks, luce
> 
> 
> 
> -- 
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> http://galaxyproject.org/wiki/
> 

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