Tetraploid Dataset Type

Objective

Provide the ability for a user to upload a dataset type of 'nucleotide_4_letter' as per other data types, similar to 'nucleotide_2_letter'.

User Story

As a GDM user, I want to be able to load a new dataset type,  'nucleotide_4_letter'

• new dataset type of 'nucleotide_4_letter'
  • available in the LoaderUI dropdown list on the 'Create' dataset page
  • dataset type of 'nucleotide_4_letter'
  • added to the cv table with cvgroup_id = 1
• Contains exactly 4 elements
  • either 0 or 1 separator character between each element
    • allowed separators are:
      • ,
      • |
      • /
      • no separator
  • allowed values/alleles are
    • A
    • C
    • G
    • T
    • N
    • +
    • -
    • anything in the missingIndicators.txt file
      • add ? to the above file
      • anything in this file that appears in the nucleotide_4_letter matrix file, replace whole 'segment' with an N, not just one element
      • locationt: http://gobiin1.bti.cornell.edu:6083/projects/GM/repos/gobiiscripts/browse/loaders/etc/missingIndicators.txt
• New type transformation in Digest/Extract similar to 'nucleotide_2_letter'.

Acceptance Criteria:

• querying the database: select * from cv where cvgroup_id = 1; results in  'nucleotide_4_letter'  in the cv table
• 'nucleotide_4_letter' is selectable in the LoaderUI dropdown list on the 'Create' dataset page
• I can successfully load a matrix with the allowed alleles and separators as described above
• any attempted load with alleles other than listed above will fail
• any attempted load with separators other than those listed above will fail
• ? has been added to the missingIndicators.txt file

Success metrics

Assumptions

Requirements

User interaction and design

Open Questions

Out of Scope