Q About 'Compute' Tool

Question: Q About 'Compute' Tool

7.1 years ago by

Ian Donaldson • 120 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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modified 7.1 years ago by Russell Bell • 30 • written 7.1 years ago by Ian Donaldson • 120

7.1 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

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

ADD COMMENT • link written 7.1 years ago by Daniel Blankenberg ♦♦ 1.7k

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. Thanks, Ian ________________________________ 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 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http: usegalaxy.org="">. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD REPLY • link written 7.1 years ago by Ian Donaldson • 120

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

ADD REPLY • link written 7.1 years ago by Hotz, Hans-Rudolf • 1.8k

7.1 years ago by

Russell Bell • 30

Russell Bell • 30 wrote:

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

ADD COMMENT • link written 7.1 years ago by Russell Bell • 30

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 ________________________________________ 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

ADD REPLY • link written 7.1 years ago by Ian Donaldson • 120

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD REPLY • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

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