On 10/10/2011 04:45 PM, Ian Donaldson wrote:
Thanks, but not quite what i need.

If i start with two intervals:
chr1    500    1000    geneA    .    +
chr1    2000    2500    geneB    .    -

I want to add via, e.g. 'Compute', the TSS position to the end of each line.  
The desired result being:

chr1    500    1000    geneA    .    +    500
chr1    2000    2500    geneB    .    -    2500

This is because geneA is on the '+' strand and geneB is on the '-' strand.


Hi Ian

Have you tried

"Filter and Sort"-> "Filter" data on any column using simple expressions

and create two lists containing all genes on the '+' strand and alles genes on the '-' strand.

followed by
"Text Manipulation"-> "Cut" columns from a table

  using 'c1,c2,c3,c4,c5,c6,c2' for the list with all genes on the '+'
                               strand

  and

  using 'c1,c2,c3,c4,c5,c6,c3' for the list with all genes on the '-'
                               strand


and then you can create a single list again with

"Text Manipulation"-> "Concatenate" datasets tail-to-head


I guess this is waht you want, isn't-it?


Regards, Hans


Thanks,
Ian
________________________________
From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: 10 October 2011 14:34
To: Ian Donaldson
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Q about 'Compute' tool

Hi Ian,

Under Operate on Genomic Intervals, you can try the "Get Flanks" tool; you can 
request upstream, downstream, or both of your provided regions. Please let us know if you 
need additional assistance.


Thanks for using Galaxy,

Dan


On Oct 10, 2011, at 6:35 AM, Ian Donaldson wrote:

Hi,

Can 'if' statements by used in 'Text manipulation'>  'Compute'?

The reason is that i have a interval file of UCSC genes, i want to identify the 
TSS of each and make a new interval reflecting the TSS position for each gene.  
But because the TSS of a '-' stranded gene is actually the 'end' coord i want 
to be able to check the strand in the compute statement.

Is this possible or is there an easier way to do this inside GALAXY?

Thank you,
Ian
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