Hello Ian,

The Compute tool accepts python operator functions. These functions are applied individually to each line in the input dataset.


In the Compute tool's help (lower portion of the form), simple examples are shown that demonstrate how the variables c1, c2, etc. will be interpreted as the column values in the input tabular dataset.

A suggested reference for syntax is this web resource:
http://docs.python.org/library/stdtypes.html#boolean-operations-and-or-not

Hopefully this helps,

Best,

Jen
Galaxy team

On 10/11/11 3:57 AM, Ian Donaldson wrote:
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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