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Question: Subtract one data set from another
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gravatar for mcrabtree
9 months ago by
mcrabtree • 10
mcrabtree • 10 wrote:

Is there a text manipulation tool or other tool that allows subtraction upon a data set by another data set that is aligned?

For example, if a defined column in two data sets were:

File #1: A,B,C,D,E,F,G,H,I,J,K,L,M

File #2: B,D,K,L

[File #1] - [File #2] = A,C,E,F,G,H,I,J,M

This shouldn't be too hard to do. Is there a tool that does this?
merge text-manipulation subtract filter cut • 313 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by mcrabtree • 10
0
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Would keeping just the specified columns from File #1 be enough? If so, the tool Cut could be used.

If you need to also filter, and just keep lines from File #1 that exist in File #2 (matched on all of the common keys), try this:

  1. Restructure each file so that columns B, D, K, L are combined into a single column.
    • Use the tool Merge Columns together.
    • You'll do this twice, once for each file.
    • This creates a new common "combined" field in the last column of each file. The original columns are left intact.
  2. Filter File #1 using File #2 on the common field created in step 1.
    • Use the tool Join two files with the option Output lines appearing in set to 1st but not in 2nd file.
  3. The result will have all of the original columns from File #1 plus the combined key used for filtering.
    • Use the Cut tool to just keep the columns you want.

If this is something that you'll be doing a few times, placing this manipulation into a workflow would make it easier to rerun all in one step. The Galaxy 101 shows how to create workflows: https://galaxyproject.org/tutorials/g101/#creating-and-editing-a-workflow

All tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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