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 <[email protected]>
>To: Ian Donaldson <[email protected]>, Daniel Blankenberg
> <[email protected]>, "[email protected]"
> <[email protected]>
>Subject: Re: [galaxy-user] Q about 'Compute' tool
>Message-ID: <[email protected]>
>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 [[email protected]]
>> Sent: 10 October 2011 14:34
>> To: Ian Donaldson
>> Cc: [email protected]
>> 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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