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Make a consistent way to deal with complicated column formats #31

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mikegloudemans opened this issue May 4, 2020 · 2 comments
Open

Make a consistent way to deal with complicated column formats #31

mikegloudemans opened this issue May 4, 2020 · 2 comments
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code-base Maintaining reasonable and intuitive code enhancement New feature or request munge Pertaining to the "munge" module usability Making tools more intuitive for the user
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v2

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@mikegloudemans
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Probably the best way to do this will be to make it so that attributes like "rsid_index" or "or_index" or "effect_allele_index" can be specified as objects with attributes

  • split_char (list of strings) [characters on which to split the column entry, could be more than one]
  • ignore_chars (list of strings) [characters to remove completely]
  • split_index (integer) [1-based index of the field to grab after splitting on split_char]

This is already done for a few traits using an rsid_split object, but in an ad-hoc way not generalized to other attribute columns

Should be able to do this for ANY column. Ref and alt too.
@mikegloudemans mikegloudemans added enhancement New feature or request munge Pertaining to the "munge" module usability Making tools more intuitive for the user code-base Maintaining reasonable and intuitive code labels May 4, 2020
@mikegloudemans
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See also: #32

@mikegloudemans mikegloudemans mentioned this issue May 4, 2020
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mikegloudemans commented May 4, 2020 •
edited

Pull ref and alt alleles from traits with unconventional formats

  • Multiple-Traits_Gurdasani_2019
  • Osteoarthritis_Zeggini_2012
  • Sarcoidosis_Rivera_2016

@mikegloudemans mikegloudemans added this to the v2 milestone May 4, 2020
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code-base Maintaining reasonable and intuitive code enhancement New feature or request munge Pertaining to the "munge" module usability Making tools more intuitive for the user
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