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Custom output format files #194

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inodb opened this issue Jun 14, 2022 · 2 comments
Open
4 tasks

Custom output format files #194

inodb opened this issue Jun 14, 2022 · 2 comments

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@inodb
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inodb commented Jun 14, 2022

Allow changing the column names etc using a supplied output format file

Some of the output formats could be:

  • tcga: https://docs.cbioportal.org/file-formats/#extended-maf-format. List all 37 first and anything extra goes in the back alphabetically
  • minimal: whatever was inputted and newly annotated columns by genome nexus
  • gdc: ??? Not sure what this should be yet. (They might have a few additional columns beyond tcga, 126 columns)
  • any custom ordering of columns (already implemented)
@ozguzMete
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#198

magically removing empty columns is much more difficult hence the data is row-based. Doable but painful... if the output format is enough for most of the time, we can skip this part

@ozguzMete
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I have added tcga and minimal to the #198

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