Thank Russell for the tip, it was just what i needed.  Is there a explanation 
of how to construct the instructions for 'Compute' somewhere?  I have not been 
able to find it.

Also thanks to Hans-Rudolf.

Ian
________________________________________
From: Russell Bell [russell.b...@hci.utah.edu]
Sent: 10 October 2011 18:16
To: galaxy-user@lists.bx.psu.edu; Ian Donaldson
Subject: Re: [galaxy-user] Q about 'Compute' tool

Ian,

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

problem i was able to get

chr1    500    1000    geneA    .    +     500.0
chr1    2000    2500    geneB    .    -     2500.0

Using

        c2 if c6=='+' else c3

in the Compute tool.  See if it works for you.

-
Russell



>Date: Mon, 10 Oct 2011 17:36:58 +0200
>From: Hans-Rudolf Hotz <h...@fmi.ch>
>To: Ian Donaldson <ian.donald...@manchester.ac.uk>,     Daniel Blankenberg
>        <d...@bx.psu.edu>,       "galaxy-user@lists.bx.psu.edu"
>        <galaxy-user@lists.bx.psu.edu>
>Subject: Re: [galaxy-user] Q about 'Compute' tool
>Message-ID: <4e93111a.4060...@fmi.ch>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>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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